Index: /issm/branches/trunk-jpl-damage/configs/config-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-altix64-castor.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-altix64-castor.sh (revision 12168) @@ -1,3 +1,3 @@ #!/bin/csh -./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/usr/include --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so +./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/usr/include --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so Index: /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh (revision 12168) @@ -0,0 +1,12 @@ +#!/bin/sh + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-vendor=arm-linux \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install Index: /issm/branches/trunk-jpl-damage/configs/config-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-cosmos.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-cosmos.sh (revision 12168) @@ -1,3 +1,3 @@ #!/bin/csh -./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm -lpthread -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/ --with-plapack-dir="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so +./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm -lpthread -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/ --with-plapack-dir="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so Index: /issm/branches/trunk-jpl-damage/configs/config-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-greenplanet.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-greenplanet.sh (revision 12168) @@ -5,19 +5,19 @@ ./configure \ - --prefix=$ISSM_TIER \ - --with-serial=no \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --prefix=$ISSM_DIR \ + --with-modules=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \ --with-mpi-lib="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-mkl-dir=/opt/intel/mkl/10.2.4.032/ \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-O3 -xS" \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh (revision 12168) @@ -2,22 +2,22 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-serial=no\ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-march=opteron -O2" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ - --with-rose-dir=$ISSM_TIER/externalpackages/rose/install/ \ - --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ + --with-rose-dir=$ISSM_DIR/externalpackages/rose/install/ \ + --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ --with-numthreads=24 \ --without-thermal \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.0.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.0.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.0.sh (revision 12168) @@ -0,0 +1,31 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.0.2 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=32 \ + --enable-debugging Index: sm/branches/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.4.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.4.sh (revision 12167) +++ (revision ) @@ -1,31 +1,0 @@ -#!/bin/sh - -#External packages versions: -#petsc 3.1 or 3.2 -#mpich 1.4 - -./configure \ - --prefix=$ISSM_TIER \ - --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ - --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ - --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-march=opteron -O2" \ - --with-numthreads=32 \ - --enable-debugging Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh (revision 12168) @@ -5,3 +5,3 @@ #mpich 1.0.2 -./configure --prefix=$ISSM_TIER --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_TIER/externalpackages/scotch/install --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_TIER/externalpackages/shapelib/install\ +./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_DIR/externalpackages/scotch/install --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_DIR/externalpackages/shapelib/install\ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 12168) @@ -3,26 +3,26 @@ #External packages versions: #petsc 3.1 or 3.2 -#mpich 1.0.2 +#mpich 1.4 ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ - --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ --with-graphics-lib=/usr/lib64/libX11.so \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh (revision 12168) @@ -2,23 +2,23 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-serial=no\ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-hypre-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-ml-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-ml-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \ - --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ + --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ --with-numthreads=24 \ --without-thermal \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-nopetsc.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-nopetsc.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo-nopetsc.sh (revision 12168) @@ -2,26 +2,26 @@ ./configure \ - --prefix=$ISSM_TIER \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --prefix=$ISSM_DIR \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib \ --with-graphics-lib=/usr/lib64/libX11.so \ - --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ --with-numthreads=18 \ --enable-debugging \ - --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install -# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +# --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ # --with-petsc-arch=$ISSM_ARCH \ -# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ -# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ -# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +# --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ +# --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +# --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +# --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +# --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +# --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-murdo.sh (revision 12168) @@ -2,24 +2,24 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ --with-numthreads=18 \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --enable-debugging Index: /issm/branches/trunk-jpl-damage/configs/config-macosx32-mathieu.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx32-mathieu.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx32-mathieu.sh (revision 12168) @@ -10,19 +10,19 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx32-ogive.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx32-ogive.sh (revision 12168) @@ -5,19 +5,19 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 12168) @@ -6,17 +6,17 @@ ./configure \ --with-serial=no\ - --prefix=$ISSM_TIER \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --prefix=$ISSM_DIR \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --without-blas-lapack-dir \ - --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-math-lib="/usr/lib/libm.dylib" \ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ - --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ - --with-adolc-dir=$ISSM_TIER/externalpackages/adolc/install/ \ + --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install/ \ --with-numthreads=8 \ --without-thermal \ @@ -34,10 +34,10 @@ #--without-prognostic \ -#--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +#--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ #--with-petsc-arch=$ISSM_ARCH \ -#--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ -#--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ -#--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ -#--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -#--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -#--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +#--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ +#--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ +#--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ +#--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +#--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +#--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-bothapis.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-bothapis.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-bothapis.sh (revision 12168) @@ -0,0 +1,33 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-nopetsc.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-nopetsc.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-nopetsc.sh (revision 12168) @@ -1,28 +1,15 @@ #!/bin/sh -#petsc 3.2 -#mpich 1.4 +pythonversion=3.2 ./configure \ - --prefix=$ISSM_TIER \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ - --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-math-lib="/usr/lib/libm.dylib" \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ - --with-numthreads=8 \ - --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install -# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ -# --with-petsc-arch=$ISSM_ARCH \ -# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ -# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ -# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ -# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-python.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-python.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-python.sh (revision 12168) @@ -5,12 +5,12 @@ ./configure \ - --prefix=$ISSM_TIER \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-python-dir=$ISSM_TIER/externalpackages/python/install\ - --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ - --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ @@ -18,12 +18,12 @@ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ --with-numthreads=8 \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ - #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - #--with-boost-dir=$ISSM_TIER/externalpackages/boost/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 12168) @@ -5,11 +5,11 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ - --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ @@ -17,11 +17,11 @@ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ --with-numthreads=8 \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ - #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-mathieu.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-mathieu.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-mathieu.sh (revision 12168) @@ -5,19 +5,19 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh (revision 12168) @@ -5,21 +5,21 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-ogive.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-ogive.sh (revision 12168) @@ -9,19 +9,19 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/gfortran/lib/x86_64/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-sophie.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-sophie.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-sophie.sh (revision 12168) @@ -9,19 +9,19 @@ ./configure \ - --prefix=$ISSM_TIER \ + --prefix=$ISSM_DIR \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-fortran-lib="/sw/usr/local/lib/x86_64/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ Index: /issm/branches/trunk-jpl-damage/configs/config-pleiades-petsc2.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-pleiades-petsc2.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-pleiades-petsc2.sh (revision 12168) @@ -2,19 +2,19 @@ ./configure \ - --prefix=$ISSM_TIER \ - --with-serial=no \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --prefix=$ISSM_DIR \ + --with-modules=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mpi-include=/nasa/sgi/mpt/1.25/include \ --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-O3 -xS" \ Index: /issm/branches/trunk-jpl-damage/configs/config-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-pleiades.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-pleiades.sh (revision 12168) @@ -2,19 +2,20 @@ ./configure \ - --prefix=$ISSM_TIER \ - --with-serial=no \ - --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --prefix=$ISSM_DIR \ + --with-modules=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ --with-mpi-include=/nasa/sgi/mpt/1.25/include \ --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-O3 -xS" \ Index: /issm/branches/trunk-jpl-damage/configs/config-win32-eric.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-win32-eric.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-win32-eric.sh (revision 12168) @@ -4,3 +4,3 @@ #get configure.sh to pick up the intel compiler -./configure --prefix=$ISSM_TIER --with-parallel=no --with-vendor=intel-win --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH +./configure --prefix=$ISSM_DIR --with-parallel=no --with-vendor=intel-win --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH Index: /issm/branches/trunk-jpl-damage/configs/config-win7-32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-win7-32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-win7-32.sh (revision 12168) @@ -2,15 +2,15 @@ #Dos style path needed for the windows sdk 7.1 cl compiler: -ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` +ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` #get configure.sh to pick up the win7 Visual Studio compiler -./configure --prefix=$ISSM_TIER \ +./configure --prefix=$ISSM_DIR \ --with-vendor=intel-win7-32 \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ - --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ - --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ + --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ + --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ + --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ - --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ - --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ + --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ + --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" Index: /issm/branches/trunk-jpl-damage/configs/config-win7-64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-win7-64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/configs/config-win7-64.sh (revision 12168) @@ -2,15 +2,15 @@ #Dos style path needed for the windows sdk 7.1 cl compiler: -ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` +ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` #get configure.sh to pick up the win7 Visual Studio compiler -./configure --prefix=$ISSM_TIER \ +./configure --prefix=$ISSM_DIR \ --with-vendor=intel-win7-64 \ --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ - --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ - --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ + --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ + --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ + --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ - --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ - --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ + --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ + --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" Index: /issm/branches/trunk-jpl-damage/configure.ac =================================================================== --- /issm/branches/trunk-jpl-damage/configure.ac (revision 12167) +++ /issm/branches/trunk-jpl-damage/configure.ac (revision 12168) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([ISSM],[4.0],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([ISSM],[4.1],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 @@ -36,6 +36,10 @@ AC_CONFIG_FILES([Makefile src/Makefile - src/c/Makefile - src/mex/Makefile + src/c/Makefile + src/py/Makefile + src/py/model/Makefile + src/modules/Makefile + src/modules/python/Makefile + src/modules/matlab/Makefile src/m/Makefile bin/Makefile]) Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_daily (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_daily (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full paths) -ISSM_DIR="/path/to/issm" -ISSM_TIER="/path/to/issm/cron/trunk-jpl" +ISSM_DIR="/path/to/issm/cron/trunk-jpl" #ISSM Architecture @@ -72,5 +71,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_nightly =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_nightly (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_nightly (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full paths) -ISSM_DIR="/path/to/issm" -ISSM_TIER="/path/to/issm/cron/trunk-jpl" +ISSM_DIR="/path/to/issm/cron/trunk-jpl" #ISSM Architecture @@ -72,5 +71,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_daily (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_daily (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full path) -ISSM_DIR="/path/to/issm/" -ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl" +ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl" #ISSM Architecture @@ -72,5 +71,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_nightly =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_nightly (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_nightly (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full path) -ISSM_DIR="/path/to/issm/" -ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl" +ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl" #ISSM Architecture @@ -72,5 +71,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/cron/configs/win732 =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/win732 (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/win732 (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full path) -ISSM_DIR="/cygdrive/c/issm" -ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" +ISSM_DIR="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" #ISSM Architecture @@ -16,5 +15,5 @@ #MATLAB path -MATLAB_PATH="C:/MATLAB/R2011b32/" +MATLAB_PATH="C:/MATLAB/R2012a/" #COMPILATION CONFIGURATION FILE @@ -32,5 +31,5 @@ # - "none" leave ISSM as is in its directory # ->skip to section 3 -ISSM_INSTALLATION="none" +ISSM_INSTALLATION="checkout" #SVN repository @@ -38,5 +37,5 @@ #execution path used for parallel runs -EXECUTION_PATH="/cygdrive/c/issm/ExecutionNightlyRun" +EXECUTION_PATH="/cygdrive/c/issm-uci/ExecutionNightlyRun" #-----------------------------------# @@ -49,6 +48,6 @@ # - "none" leave external packages as is # ->skip to section 4 -ISSM_EXTERNALPACKAGES="none" -EXTERNALPACKAGESDIR="/cygdrive/c/issm/trunk-jpl/externalpackages" +ISSM_EXTERNALPACKAGES="link" +EXTERNALPACKAGESDIR="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" #List of external pakages to be installed @@ -66,5 +65,5 @@ # - "yes" compile ISSM # - "no" do not compile ISSM -ISSM_COMPILATION="no" +ISSM_COMPILATION="yes" #----------------------# @@ -73,9 +72,9 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. -SKIPMAIL="no" +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. +SKIPMAIL="yes" #Sender email address -EMAIL_ADRESS="eric.larour@jpl.nasa.gov" +EMAIL_ADRESS="eric.larour@gmail.com" #------------------------# @@ -85,5 +84,5 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=8 +NUMCPUS_INSTALL=1 #number of cpus used in the nightly runs. @@ -95,8 +94,8 @@ #ex: "'id',[101 102 103]" -NROPTIONS="'benchmark','all'" +NROPTIONS="'benchmark',102:2:120" #------------------------# # 7: Matlab# #------------------------# -MATLABBIN=/cygdrive/c/MATLAB/R2011b32/bin/matlab +MATLABBIN=/cygdrive/c/MATLAB/R2012a/bin/matlab Index: /issm/branches/trunk-jpl-damage/cron/configs/win764 =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/win764 (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/win764 (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full path) -ISSM_DIR="/cygdrive/c/issm" -ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" +ISSM_DIR="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" #ISSM Architecture @@ -73,5 +72,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/cron/configs/winxp32 =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/winxp32 (revision 12167) +++ /issm/branches/trunk-jpl-damage/cron/configs/winxp32 (revision 12168) @@ -6,6 +6,5 @@ #ISSM main directory (full path) -ISSM_DIR="C:/home/issm/trunk-jpl" -ISSM_TIER="C:/home/issm/trunk-jpl/cron/trunk-jpl" +ISSM_DIR="C:/home/issm/trunk-jpl/cron/trunk-jpl" #ISSM Architecture @@ -66,5 +65,5 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be -#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. SKIPMAIL="no" Index: /issm/branches/trunk-jpl-damage/etc/environment.csh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment.csh (revision 12167) +++ /issm/branches/trunk-jpl-damage/etc/environment.csh (revision 12168) @@ -1,4 +1,4 @@ -#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) -source $ISSM_TIER/etc/environment_variables.csh +#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) +source $ISSM_DIR/etc/environment_variables.csh #Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables @@ -10,8 +10,8 @@ #CRON utilities -setenv PATH {$PATH}:{$ISSM_TIER}/cron +setenv PATH {$PATH}:{$ISSM_DIR}/cron #SCRIPTS utilities -setenv PATH {$PATH}:{$ISSM_TIER}/scripts +setenv PATH {$PATH}:{$ISSM_DIR}/scripts #MATLAB @@ -110,9 +110,9 @@ #AUTOCONF setenv AUTOCONF_DIR {$AUTOCONF_DIR} -setenv PATH {$PATH}:{$AUTOCONF_DIR}/bin +setenv PATH {$AUTOCONF_DIR}/bin:{$PATH} #AUTOMAKE setenv AUTOMAKE_DIR {$AUTOMAKE_DIR} -setenv PATH {$PATH}:{$AUTOMAKE_DIR}/bin +setenv PATH {$AUTOMAKE_DIR}/bin:{$PATH} #BORLAND Index: /issm/branches/trunk-jpl-damage/etc/environment.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 12168) @@ -1,10 +1,10 @@ -#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) +#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) #Windows compilers: if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then - source $ISSM_TIER/externalpackages/windows/windows_environment.sh + source $ISSM_DIR/externalpackages/windows/windows_environment.sh fi -source $ISSM_TIER/etc/environment_variables.sh +source $ISSM_DIR/etc/environment_variables.sh #Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them after exporting the variables @@ -16,8 +16,8 @@ #CRON utilities -PATH="$PATH:$ISSM_TIER/cron" +PATH="$PATH:$ISSM_DIR/cron" #scripts -PATH="$PATH:$ISSM_TIER/scripts" +PATH="$PATH:$ISSM_DIR/scripts" ##MATLAB @@ -137,5 +137,5 @@ #export INTEL_DIR #PATH="$PATH:$INTEL_DIR" -#source $ISSM_TIER/externalpackages/intel/intel.sh +#source $ISSM_DIR/externalpackages/intel/intel.sh #SDK @@ -242,6 +242,6 @@ export PATH="$PATH:$ANDROID_NDK_DIR/" -#ANDROID_DEV_DIR -export ANDROID_DEV_DIR +#ANDROID_DIR +export ANDROID_DIR #ANDROID_SDK @@ -259,6 +259,6 @@ #PYTHON export PATH="$PYTHON_DIR/bin:$PATH" -export PYTHONPATH="$PYTHONPATH:$ISSM_TIER/src/mex" -export LD_LIBRARY_PATH=$ISSM_TIER/src/mex:$LD_LIBRARY_PATH +export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python" +export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$LD_LIBRARY_PATH #MODELE Index: /issm/branches/trunk-jpl-damage/etc/environment_variables.csh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment_variables.csh (revision 12167) +++ /issm/branches/trunk-jpl-damage/etc/environment_variables.csh (revision 12168) @@ -1,77 +1,77 @@ # # -#This routine can only be run if the ISSM_TIER variable has been correctly set! +#This routine can only be run if the ISSM_DIR variable has been correctly set! # # #MATLAB -set MATLAB_DIR={$ISSM_TIER}/externalpackages/matlab/install +set MATLAB_DIR={$ISSM_DIR}/externalpackages/matlab/install #MPI -set MPI_DIR={$ISSM_TIER}/externalpackages/mpich2/install +set MPI_DIR={$ISSM_DIR}/externalpackages/mpich2/install #PETSC -set PETSC_DIR={$ISSM_TIER}/externalpackages/petsc/install +set PETSC_DIR={$ISSM_DIR}/externalpackages/petsc/install #SLEPC -set SLEPC_DIR={$ISSM_TIER}/externalpackages/slepc/install +set SLEPC_DIR={$ISSM_DIR}/externalpackages/slepc/install #Dakota -set DAKOTA_DIR={$ISSM_TIER}/externalpackages/dakota/install +set DAKOTA_DIR={$ISSM_DIR}/externalpackages/dakota/install #Qhull -set QHULL_DIR={$ISSM_TIER}/externalpackages/qhull/install +set QHULL_DIR={$ISSM_DIR}/externalpackages/qhull/install #Doxygen -set DOXYGEN_DIR={$ISSM_TIER}/externalpackages/doxygen/install +set DOXYGEN_DIR={$ISSM_DIR}/externalpackages/doxygen/install #MTOC -set MTOC_DIR={$ISSM_TIER}/externalpackages/mtoc/install +set MTOC_DIR={$ISSM_DIR}/externalpackages/mtoc/install #Triangle -set TRIANGLE_DIR={$ISSM_TIER}/externalpackages/triangle/install +set TRIANGLE_DIR={$ISSM_DIR}/externalpackages/triangle/install #METIS -set METIS_DIR={$ISSM_TIER}/externalpackages/metis/install +set METIS_DIR={$ISSM_DIR}/externalpackages/metis/install #BLAS -set BLAS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack +set BLAS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack #LAPACK -set LAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH +set LAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH #SCALAPACK -set SCALAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH +set SCALAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH #PLAPACK -set PLAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32 +set PLAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32 #BLACS -set BLACS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH +set BLACS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH #sowing -set SOWING_DIR={$ISSM_TIER}/externalpackages/sowing/install +set SOWING_DIR={$ISSM_DIR}/externalpackages/sowing/install #YAMS -set YAMS_DIR={$ISSM_TIER}/externalpackages/yams/install +set YAMS_DIR={$ISSM_DIR}/externalpackages/yams/install #TEX2IM -set TEX2IM_DIR={$ISSM_TIER}/externalpackages/tex2im/install +set TEX2IM_DIR={$ISSM_DIR}/externalpackages/tex2im/install #Chaco -set CHACO_DIR={$ISSM_TIER}/externalpackages/chaco/install +set CHACO_DIR={$ISSM_DIR}/externalpackages/chaco/install #MeshPart -set MESHPART_DIR={$ISSM_TIER}/externalpackages/meshpart/install +set MESHPART_DIR={$ISSM_DIR}/externalpackages/meshpart/install #SCOTCH -set SCOTCH_DIR={$ISSM_TIER}/externalpackages/scotch/install +set SCOTCH_DIR={$ISSM_DIR}/externalpackages/scotch/install #Development packages #automake -set AUTOMAKE_DIR={$ISSM_TIER}/externalpackages/automake/install +set AUTOMAKE_DIR={$ISSM_DIR}/externalpackages/automake/install #autoconf -set AUTOCONF_DIR={$ISSM_TIER}/externalpackages/autoconf/install +set AUTOCONF_DIR={$ISSM_DIR}/externalpackages/autoconf/install #borland @@ -79,6 +79,6 @@ #ssh -set SSH_DIR={$ISSM_TIER}/externalpackages/ssh +set SSH_DIR={$ISSM_DIR}/externalpackages/ssh #valgrind -set VALGRIND_DIR={$ISSM_TIER}/externalpackages/valgrind/install/bin +set VALGRIND_DIR={$ISSM_DIR}/externalpackages/valgrind/install/bin Index: /issm/branches/trunk-jpl-damage/etc/environment_variables.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 12168) @@ -1,83 +1,83 @@ # # -#This routine can only be run if the ISSM_TIER variable has been correctly set! +#This routine can only be run if the ISSM_DIR variable has been correctly set! # # #MATLAB -MATLAB_DIR="$ISSM_TIER/externalpackages/matlab/install" +MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" #MPI -MPI_DIR="$ISSM_TIER/externalpackages/mpich2/install" +MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" #PETSC -PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" +PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" #SLEPC -SLEPC_DIR="$ISSM_TIER/externalpackages/slepc/install" +SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" #Dakota -DAKOTA_DIR="$ISSM_TIER/externalpackages/dakota/install" +DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" #Qhull -QHULL_DIR="$ISSM_TIER/externalpackages/qhull/install" +QHULL_DIR="$ISSM_DIR/externalpackages/qhull/install" #Doxygen -DOXYGEN_DIR="$ISSM_TIER/externalpackages/doxygen/install" +DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" #MTOC -MTOC_DIR="$ISSM_TIER/externalpackages/mtoc/install" +MTOC_DIR="$ISSM_DIR/externalpackages/mtoc/install" #Triangle -TRIANGLE_DIR="$ISSM_TIER/externalpackages/triangle/install" +TRIANGLE_DIR="$ISSM_DIR/externalpackages/triangle/install" #METIS -METIS_DIR="$ISSM_TIER/externalpackages/metis/install" +METIS_DIR="$ISSM_DIR/externalpackages/metis/install" #BLAS -BLAS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack" +BLAS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack" #LAPACK -LAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH" +LAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH" #SCALAPACK -SCALAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH" +SCALAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH" #PLAPACK -PLAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32" +PLAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32" #BLACS -BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" +BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" #sowing -SOWING_DIR="$ISSM_TIER/externalpackages/sowing/install" +SOWING_DIR="$ISSM_DIR/externalpackages/sowing/install" #BLACS -BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" +BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" #YAMS -YAMS_DIR="$ISSM_TIER/externalpackages/yams/install" +YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" #BAMG -BAMG_DIR="$ISSM_TIER/externalpackages/bamg/install" +BAMG_DIR="$ISSM_DIR/externalpackages/bamg/install" #Chaco -CHACO_DIR="$ISSM_TIER/externalpackages/chaco/install" +CHACO_DIR="$ISSM_DIR/externalpackages/chaco/install" #MeshPart -MESHPART_DIR="$ISSM_TIER/externalpackages/meshpart/install" +MESHPART_DIR="$ISSM_DIR/externalpackages/meshpart/install" #SCOTCH -SCOTCH_DIR="$ISSM_TIER/externalpackages/scotch/install" +SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install" #Development packages #automake -AUTOMAKE_DIR="$ISSM_TIER/externalpackages/automake/install" +AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install" #libtool -LIBTOOL_DIR="$ISSM_TIER/externalpackages/libtool/install" +LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install" #autoconf -AUTOCONF_DIR="$ISSM_TIER/externalpackages/autoconf/install" +AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install" #borland @@ -88,5 +88,5 @@ #TEX2IM -TEX2IM_DIR="$ISSM_TIER/externalpackages/tex2im/install" +TEX2IM_DIR="$ISSM_DIR/externalpackages/tex2im/install" #sdk @@ -94,40 +94,40 @@ #ssh -SSH_DIR="$ISSM_TIER/externalpackages/ssh" +SSH_DIR="$ISSM_DIR/externalpackages/ssh" #valgrind -VALGRIND_DIR="$ISSM_TIER/externalpackages/valgrind/install/bin" +VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin" #graphviz -GRAPHVIZ_DIR="$ISSM_TIER/externalpackages/graphviz/install/bin" +GRAPHVIZ_DIR="$ISSM_DIR/externalpackages/graphviz/install/bin" #cppcheck -CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install" +CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" #gdal -GDAL_DIR="$ISSM_TIER/externalpackages/gdal/install" +GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" #mercurial -MERCURIAL_DIR="$ISSM_TIER/externalpackages/mercurial/install" +MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" #boost -BOOST_DIR="$ISSM_TIER/externalpackages/boost/install" -BOOSTROOT="$ISSM_TIER/externalpackages/boost/install" +BOOST_DIR="$ISSM_DIR/externalpackages/boost/install" +BOOSTROOT="$ISSM_DIR/externalpackages/boost/install" #OpenAnalysis -OPENANALYSISROOT="$ISSM_TIER/externalpackages/openanalysis/install" +OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install" #xerces -XERCESROOT="$ISSM_TIER/externalpackages/xerces/install" -XERCESCROOT="$ISSM_TIER/externalpackages/xerces/src" +XERCESROOT="$ISSM_DIR/externalpackages/xerces/install" +XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src" #xaifBooster -XAIFBOOSTERROOT="$ISSM_TIER/externalpackages/xaifbooster/" -XAIF_DIR="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster" -XAIFBOOSTER_HOME="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster" +XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/" +XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" +XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" PLATFORM=x86-Linux #angel -ANGELROOT="$ISSM_TIER/externalpackages/angel/angel" +ANGELROOT="$ISSM_DIR/externalpackages/angel/angel" #java @@ -135,63 +135,63 @@ #bbftp -BBFTP_DIR="$ISSM_TIER/externalpackages/bbftp/install" +BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install" #adic2 -ADIC_DIR="$ISSM_TIER/externalpackages/adic/install" +ADIC_DIR="$ISSM_DIR/externalpackages/adic/install" #colpack -COLPACK_DIR="$ISSM_TIER/externalpackages/colpack/install" +COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install" #eclipse -ECLIPSE_DIR="$ISSM_TIER/externalpackages/eclipse/install" +ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install" #flaim -FLAIM_DIR="$ISSM_TIER/externalpackages/flaim/install" +FLAIM_DIR="$ISSM_DIR/externalpackages/flaim/install" #appscan -APPSCAN_DIR="$ISSM_TIER/externalpackages/appscan" +APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan" #cppcheck -CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install" +CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" #rats -RATS_DIR="$ISSM_TIER/externalpackages/rats/install" +RATS_DIR="$ISSM_DIR/externalpackages/rats/install" #dyson -DYSON_DIR="$ISSM_TIER/externalpackages/dyson/" +DYSON_DIR="$ISSM_DIR/externalpackages/dyson/" #cmake -CMAKE_DIR="$ISSM_TIER/externalpackages/cmake/install" +CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" #shapelib -SHAPELIB_DIR="$ISSM_TIER/externalpackages/shapelib/install" +SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install" #cccl -CCCL_DIR="$ISSM_TIER/externalpackages/cccl/install" +CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install" #packagemaker -PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install" +PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install" + +#android-dev-dir +ANDROID_DIR="$ISSM_DIR/externalpackages/android" #android-ndk -ANDROID_NDK_DIR="$ISSM_TIER/externalpackages/android-ndk/install" - -#android-dev-dir -ANDROID_DEV_DIR="$ISSM_TIER/externalpackages/android-dev-dir" +ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" #android-sdk -ANDROID_SDK_DIR="$ISSM_TIER/externalpackages/android-sdk/install-sdk" +ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk" #android-ant -ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant" +ANDROID_ANT_DIR="$ANDROID_DIR/android-sdk/install-ant" #gsl -GSL_DIR="$ISSM_TIER/externalpackages/gsl/install" +GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" #gnu make -GMAKE_DIR="$ISSM_TIER/externalpackages/gmake/install" +GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install" #PYTHON -PYTHON_DIR="$ISSM_TIER/externalpackages/python/install" +PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" #MODELE -MODELE_DIR="$ISSM_TIER/externalpackages/modelE" +MODELE_DIR="$ISSM_DIR/externalpackages/modelE" Index: /issm/branches/trunk-jpl-damage/externalpackages/adic/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/adic/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/adic/install.sh (revision 12168) @@ -19,11 +19,11 @@ cd build ../source/configure \ - --with-rose=$ISSM_TIER/externalpackages/rose/install \ - --with-openanalysis=$ISSM_TIER/externalpackages/openanalysis/openanalysis/x86_64-Linux \ - --with-boost=$ISSM_TIER/externalpackages/boost/install \ - --with-xerces=$ISSM_TIER/externalpackages/xerces/src \ - --with-xaifbooster=$ISSM_TIER/externalpackages/xaifbooster/xaifBooster \ - --with-colpack=$ISSM_TIER/externalpackages/colpack/install\ - --prefix=$ISSM_TIER/externalpackages/adic/install + --with-rose=$ISSM_DIR/externalpackages/rose/install \ + --with-openanalysis=$ISSM_DIR/externalpackages/openanalysis/openanalysis/x86_64-Linux \ + --with-boost=$ISSM_DIR/externalpackages/boost/install \ + --with-xerces=$ISSM_DIR/externalpackages/xerces/src \ + --with-xaifbooster=$ISSM_DIR/externalpackages/xaifbooster/xaifBooster \ + --with-colpack=$ISSM_DIR/externalpackages/colpack/install\ + --prefix=$ISSM_DIR/externalpackages/adic/install if [ -z $1 ]; then make Index: /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 12168) @@ -20,5 +20,5 @@ ./configure \ - --prefix=$ISSM_TIER/externalpackages/adolc/install \ + --prefix=$ISSM_DIR/externalpackages/adolc/install \ --enable-sparse \ --enable-docexa \ Index: /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 12168) @@ -15,5 +15,5 @@ #Compile autoconf cd src -./configure --prefix="$ISSM_TIER/externalpackages/autoconf/install" +./configure --prefix="$ISSM_DIR/externalpackages/autoconf/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh (revision 12168) @@ -13,5 +13,5 @@ #Compile automake cd src -./configure --prefix="$ISSM_TIER/externalpackages/automake/install" +./configure --prefix="$ISSM_DIR/externalpackages/automake/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 12168) @@ -19,5 +19,5 @@ #Configure and compile cd bbftpc -./configure --prefix=$ISSM_TIER/externalpackages/bbftp/install +./configure --prefix=$ISSM_DIR/externalpackages/bbftp/install make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh (revision 12168) @@ -22,7 +22,7 @@ cd src ./bootstrap.sh \ - --prefix="$ISSM_TIER/externalpackages/boost/install" \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ --with-python=python3.2 \ - --with-python-root="$ISSM_TIER/externalpackages/python/install" + --with-python-root="$ISSM_DIR/externalpackages/python/install" #Compile boost Index: /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh (revision 12168) @@ -13,5 +13,5 @@ cd src -./configure --prefix="$ISSM_TIER/externalpackages/bsdtar/install" +./configure --prefix="$ISSM_DIR/externalpackages/bsdtar/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh (revision 12168) @@ -15,5 +15,5 @@ #Compile -./configure --prefix="$ISSM_TIER/externalpackages/cccl/install" +./configure --prefix="$ISSM_DIR/externalpackages/cccl/install" make Index: /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 12168) @@ -14,5 +14,5 @@ #Compile cmake cd install -./bootstrap --prefix=$ISSM_TIER/externalpackages/cmake/install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install if [ -z $1 ]; then make Index: /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 12168) @@ -17,4 +17,4 @@ make -j $1 fi -make install PREFIX=$ISSM_TIER/externalpackages/cppcheck/install +make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install cd .. Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 12168) @@ -29,5 +29,5 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ --without-graphics \ --with-pic \ Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 12168) @@ -29,5 +29,5 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ --without-graphics \ --with-pic \ Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh (revision 12168) @@ -29,5 +29,5 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ --without-graphics \ --with-pic \ Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 12168) @@ -29,10 +29,10 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ --without-graphics \ --with-pic \ --disable-mpi \ - --with-blas="-L$ISSM_TIER/externalpackages/petsc/install/lib -lfblas " \ - --with-lapack="-L$ISSM_TIER/externalpackages/petsc/install/lib -lflapack -lPLAPACK " + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack -lPLAPACK " cd .. Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 12168) @@ -29,5 +29,5 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ --without-graphics \ --with-pic \ Index: /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh (revision 12168) @@ -0,0 +1,4 @@ +#!/bin/bash + +curl -O http://python-distribute.org/distribute_setup.py +python distribute_setup.py Index: /issm/branches/trunk-jpl-damage/externalpackages/doxygen/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/doxygen/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/doxygen/install.sh (revision 12168) @@ -8,5 +8,5 @@ #Configure doxygen -cd install && ./configure --prefix "$ISSM_TIER/externalpackages/doxygen/install" +cd install && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" if [ -z $1 ]; then make Index: /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh (revision 12168) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf install +rm -rf freetype-2.4.9 +mkdir src install + +#Untar +tar -zxvf freetype-2.4.9.tar.gz + +#Move freetype into src directory +mv freetype-2.4.9/* src +rm -rf freetype-2.4.9 + +#Configure freetype +cd src +sudo ./configure + +#Compile and install freetype +if [ -z $1 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 12168) @@ -17,5 +17,5 @@ cd src ./configure \ - --prefix="$ISSM_TIER/externalpackages/gdal/install" \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ --without-python \ --with-netcdf=no \ Index: /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh (revision 12168) @@ -16,5 +16,5 @@ #Configure and compile: -./configure --prefix=$ISSM_TIER/externalpackages/gmake/install +./configure --prefix=$ISSM_DIR/externalpackages/gmake/install if [ -z $1 ]; then Index: /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 12168) @@ -14,5 +14,5 @@ #Configure dakota cd src -./configure --prefix="$ISSM_TIER/externalpackages/graphviz/install" +./configure --prefix="$ISSM_DIR/externalpackages/graphviz/install" cd .. Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh (revision 12168) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc\ + LD=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ld\ + AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar\ + RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib\ + NM=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-nm\ + OBJ_EXT=o\ + LIB_EXT=a\ + --host="arm-linux"\ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ -z $1 ]; then + make +else + make -j $1 +fi + +make install Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64-murdo.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64-murdo.sh (revision 12168) @@ -16,5 +16,5 @@ ./configure \ - --prefix="$ISSM_TIER/externalpackages/gsl/install" + --prefix="$ISSM_DIR/externalpackages/gsl/install" #Compile gsl Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh (revision 12168) @@ -18,5 +18,5 @@ ./configure \ - --prefix="$ISSM_TIER/externalpackages/gsl/install" + --prefix="$ISSM_DIR/externalpackages/gsl/install" #Compile gsl Index: /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh (revision 12168) @@ -0,0 +1,19 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf install +rm -rf ipython-0.12 +mkdir src install + +#Untar +tar -zxvf ipython-0.12.tar.gz + +#Move ipython into src directory +mv ipython-0.12/* src +rm -rf ipython-0.12 + +#install ipython +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 12168) @@ -10,4 +10,4 @@ #Compile cd install -export PREFIX="$ISSM_TIER/externalpackages/latex2rtf/install/" +export PREFIX="$ISSM_DIR/externalpackages/latex2rtf/install/" make Index: /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh (revision 12168) @@ -0,0 +1,13 @@ +#!/bin/bash + +#Some cleanup +rm -rf install +rm -rf libermate-0.4 +mkdir install + +#Untar +tar -zxvf libermate-0.4.tgz + +#Move libermate into install directory +mv libermate-0.4/* install +rm -rf libermate-0.4 Index: /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh (revision 12168) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf install +rm -rf libpng-1.5.10 +mkdir src install + +#Untar +tar -zxvf libpng-1.5.10.tar.gz + +#Move libpng into src directory +mv libpng-1.5.10/* src +rm -rf libpng-1.5.10 + +#Configure libpng +cd src +sudo ./configure + +#Compile and install libpng +if [ -z $1 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 12168) @@ -13,5 +13,5 @@ #Compile libtool cd src -./configure --prefix="$ISSM_TIER/externalpackages/libtool/install" +./configure --prefix="$ISSM_DIR/externalpackages/libtool/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 12168) @@ -5,9 +5,8 @@ #Select or create a new simlink -#ln -s /usr/local/pkgs/matlab-7.6/ install +ln -s /usr/local/pkgs/matlab-7.6/ install #ln -s /usr/local/matlab704/ install #ln -s /usr/local/matlab711/ install ln -s /usr/local/matlab712/ install -#ln -s /usr/local/pkgs/matlab-7.6/ install # Macintosh (OSX) simlink @@ -16,3 +15,3 @@ #ln -s /Applications/MATLAB_R2010a.app/ install #ln -s /Applications/MATLAB_R2012a.app/ install -ln -s /Applications/MATLAB*.app/ install +#ln -s /Applications/MATLAB*.app/ install Index: /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install.sh (revision 12168) @@ -0,0 +1,7 @@ +#/bin/bash + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 12168) @@ -17,4 +17,4 @@ #Compile metis -make config prefix="$ISSM_TIER/externalpackages/metis/install" +make config prefix="$ISSM_DIR/externalpackages/metis/install" make install Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12168) @@ -18,5 +18,5 @@ export FFLAGS="$FFLAGS -fPIC" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-sharedlibs=gcc \ --enable-f91=gfortran Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12168) @@ -18,5 +18,5 @@ export FFLAGS="$FFLAGS -fPIC" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-sharedlibs=gcc \ --enable-f91=gfortran Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12168) @@ -17,5 +17,5 @@ export CFLAGS=" -m32" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-f91=gfortran \ --enable-sharedlibs=osx-gcc Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12168) @@ -17,5 +17,5 @@ export CFLAGS="$CFLAGS -fPIC" export FFLAGS="$FFLAGS -fPIC" -./configure --prefix="$ISSM_TIER/externalpackages/mpich2/install" +./configure --prefix="$ISSM_DIR/externalpackages/mpich2/install" #Apply Patch to examples Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 12168) @@ -17,5 +17,5 @@ export FFLAGS="$FFLAGS -fPIC" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-shared \ --enable-sharedlibs=gcc \ Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12168) @@ -19,5 +19,5 @@ export CPPFLAGS=" -arch i386" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-f91=gfortran \ --enable-sharedlibs=osx-gcc \ Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12168) @@ -19,5 +19,5 @@ export CXXFLAGS=" -arch x86_64" ./configure \ - --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ --enable-f91 \ --enable-sharedlibs=osx-gcc \ Index: /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 12168) @@ -15,9 +15,9 @@ cd install ./configure \ - --prefix "$ISSM_TIER/externalpackages/ncview/install" \ + --prefix "$ISSM_DIR/externalpackages/ncview/install" \ --x-libraries=/usr/X11/lib/ \ --x-includes=/usr/X11/include/ \ - --with-netcdf_incdir="$ISSM_TIER/externalpackages/netcdf/install/include/" \ - --with-netcdf_libdir="$ISSM_TIER/externalpackages/netcdf/install/lib/" + --with-netcdf_incdir="$ISSM_DIR/externalpackages/netcdf/install/include/" \ + --with-netcdf_libdir="$ISSM_DIR/externalpackages/netcdf/install/lib/" make Index: /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 12168) @@ -15,5 +15,5 @@ #Configure and compile cd install -./configure --prefix="$ISSM_TIER/externalpackages/netcdf/install" +./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" if [ -z $1 ]; then make Index: /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh (revision 12168) @@ -1,10 +1,27 @@ #/bin/bash -#Install Python3 nose module +#Install Python nose module -rm -rf py3k +pythonversion=2 + +rm -rf src -svn checkout http://python-nose.googlecode.com/svn/branches/py3k -cd py3k +if [[ $pythonversion == "3" ]];then -python3.2 ./setup.py build -python3.2 ./setup.py install + svn checkout http://python-nose.googlecode.com/svn/branches/py3k + mv py3k src + + cd src + python ./setup.py build + python ./setup.py install +fi + +if [[ $pythonversion == "2" ]];then + + tar -zxvf nose-1.1.2.tar.gz + mv nose-1.1.2 src + rm -rf nose-1.1.2 + + cd src + python ./setup.py build + python ./setup.py install +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 12168) @@ -13,5 +13,5 @@ #Configure doxygen cd install -./configure --prefix "$ISSM_TIER/externalpackages/python/install" +./configure --prefix "$ISSM_DIR/externalpackages/python/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12168) @@ -17,5 +17,5 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --ISSM_ARCH=$ISSM_ARCH \ @@ -41,5 +41,5 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --ISSM_ARCH=$ISSM_ARCH \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12168) @@ -12,5 +12,5 @@ #configure cd install -PETSC_DIR=$ISSM_TIER/externalpackages/petsc/install +PETSC_DIR=$ISSM_DIR/externalpackages/petsc/install ./config/configure.py \ --prefix=$PETSC_DIR \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12168) @@ -13,8 +13,8 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=linux-gnu-amd64 \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-fc=gfortran \ --with-debugging=1 \ @@ -25,5 +25,5 @@ --download-blas=yes \ --download-f-blas-lapack=yes \ - --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ + --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ --download-plapack=yes \ --COPTFLAGS="-march=opteron -O2" \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12168) @@ -17,8 +17,8 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=macosx-gnu \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-fc=/usr/local/bin/gfortran \ --with-debugging=0 \ @@ -29,5 +29,5 @@ --download-blas=yes \ --download-f-blas-lapack=yes \ - --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ --download-plapack=yes \ --CXXFLAGS=" -fPIC -arch i386" \ @@ -43,17 +43,17 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=macosx-gnu \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-fc=/usr/local/bin/gfortran \ --with-debugging=0 \ --with-shared=0 \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3 \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3 \ --download-scalapack=yes \ --download-blacs=yes \ --download-blas=yes \ --download-f-blas-lapack=yes \ - --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ --download-plapack=yes \ --CXXFLAGS=" -fPIC -arch i386" \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12168) @@ -12,8 +12,8 @@ #configure cd install -./config/configure.py --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ +./config/configure.py --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=macosx-gnu \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-fc=/usr/local/bin/gfortran \ --with-debugging=0 \ @@ -24,5 +24,5 @@ --download-blas=yes \ --download-f-blas-lapack=yes \ - --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \ --download-plapack=yes Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12168) @@ -13,8 +13,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --PETSC_ARCH=macosx-gnu \ - --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ --with-debugging=0 \ --with-shared-libraries=0 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12168) @@ -17,5 +17,5 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH=$ISSM_ARCH \ @@ -44,5 +44,5 @@ cd install ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH=$ISSM_ARCH \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12168) @@ -14,7 +14,7 @@ ./config/configure.py \ --with-parallel-no \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --PETSC_ARCH=cygwin-intel \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-debugging=0 \ --with-mpi=0 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh (revision 12168) @@ -14,7 +14,7 @@ ./config/configure.py \ --with-parallel-no \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --PETSC_ARCH=cygwin-intel \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ --with-debugging=0 \ --with-mpi=0 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12168) @@ -17,6 +17,6 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --ISSM_ARCH=$ISSM_ARCH \ --with-debugging=no \ @@ -41,6 +41,6 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-batch=1 \ --ISSM_ARCH=$ISSM_ARCH \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 12168) @@ -13,6 +13,6 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-batch=1 \ --ISSM_ARCH=$ISSM_ARCH \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12168) @@ -13,8 +13,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=linux-gnu-amd64 \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-shared=0 \ @@ -25,5 +25,5 @@ --download-f-blas-lapack=yes \ --download-parmetis=yes \ - --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ + --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ --download-plapack=yes \ --COPTFLAGS="-march=opteron -O2" \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12168) @@ -13,8 +13,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --PETSC_ARCH=macosx-gnu \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --with-debugging=0 \ --with-shared=0 \ @@ -25,5 +25,5 @@ --download-f-blas-lapack=yes \ --download-plapack=yes \ - --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \ --COPTFLAGS="-march=opteron -O2 -arch i386" \ --FOPTFLAGS="-march=opteron -O2 -arch i386" \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12168) @@ -13,7 +13,7 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --PETSC_ARCH=macosx-gnu \ --with-fc=/usr/local/bin/gfortran \ @@ -30,5 +30,5 @@ --FOPTFLAGS="-march=opteron -O2 " \ --CXXOPTFLAGS="-march=opteron -O2 " \ - --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " #Compile petsc and install it Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 12168) @@ -17,8 +17,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=no \ --with-shared=0 \ @@ -44,8 +44,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=no \ --with-shared=0 \ @@ -57,5 +57,5 @@ --download-scalapack=yes \ --download-blacs=yes \ - --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ + --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ --download-parmetis=yes \ --FFLAGS=-I/usr/include \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh (revision 12168) @@ -14,7 +14,7 @@ ./config/configure.py \ --with-parallel-no \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --PETSC_ARCH=cygwin-intel \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-mpi=0 \ @@ -26,8 +26,8 @@ #./config/configure.py \ -# --prefix="$ISSM_TIER/externalpackages/petsc/install" \ -# --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ +# --prefix="$ISSM_DIR/externalpackages/petsc/install" \ +# --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ # --PETSC_ARCH=macosx-gnu \ -# --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ +# --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ # --with-debugging=0 \ # --with-shared=0 \ @@ -38,5 +38,5 @@ # --download-f-blas-lapack=yes \ # --download-plapack=yes \ -# --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \ +# --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \ # --COPTFLAGS="-march=opteron -O2 -arch i386" \ # --FOPTFLAGS="-march=opteron -O2 -arch i386" \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12168) @@ -13,6 +13,6 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --PETSC_ARCH="$ISSM_ARCH" \ --with-batch=1 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 12168) @@ -13,9 +13,9 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ --with-clanguage=C++ \ --PETSC_ARCH=linux-gnu-amd64 \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-shared-libraries=0 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 12168) @@ -13,8 +13,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --PETSC_ARCH=macosx-gnu \ - --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ --with-debugging=0 \ --with-shared-libraries=0 \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 12168) @@ -17,8 +17,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-shared-libraries=0 \ @@ -44,8 +44,8 @@ cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-batch=1 \ --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-shared-libraries=0 \ @@ -57,5 +57,5 @@ --download-scalapack=yes \ --download-blacs=yes \ - --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ + --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ --download-parmetis=yes \ --FFLAGS=-I/usr/include \ Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-dev-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-dev-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-dev-linux64.sh (revision 12168) @@ -6,4 +6,5 @@ # Adapted from petsc 3.2. # Used Mercurial to get code + rm -rf src hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src cd src @@ -25,11 +26,12 @@ if [ $STEP -eq 2 ]; then + rm -rf install cd src ./config/configure.py \ - --prefix="$ISSM_TIER/externalpackages/petsc/install" \ - --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ --with-clanguage=C++ \ --PETSC_ARCH=linux-gnu-amd64 \ - --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ --with-shared-libraries=0 \ @@ -42,4 +44,5 @@ --download-plapack=yes \ --download-parmetis=yes \ + --download-spai=yes \ --with-pic=1 Index: /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh (revision 12168) @@ -0,0 +1,18 @@ +#!/bin/bash + +#Some cleanup +rm -rf install +rm -rf pyclips-1.0.7.348 +mkdir install + +#Untar +tar -zxvf pyclips-1.0.7.348.tar.gz + +#Move pyclips into install directory +mv pyclips/* install +rm -rf pyclips + +#install +cd install +python setup.py build +sudo python setup.py install Index: /issm/branches/trunk-jpl-damage/externalpackages/python/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/python/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/python/install.sh (revision 12168) @@ -20,5 +20,5 @@ #Configure doxygen cd src -./configure --prefix="$ISSM_TIER/externalpackages/python/install" --enable-framework="$ISSM_TIER/externalpackages/python/install" +./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" if [ -z $1 ]; then make Index: /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 12168) @@ -15,5 +15,5 @@ #Configure qhull cd src -./configure --prefix="$ISSM_TIER/externalpackages/qhull/install" +./configure --prefix="$ISSM_DIR/externalpackages/qhull/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh (revision 12168) @@ -12,5 +12,5 @@ #compile cd src -./configure --prefix=$ISSM_TIER/externalpackages/rats/install +./configure --prefix=$ISSM_DIR/externalpackages/rats/install make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh (revision 12168) +++ /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh (revision 12168) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf readline-6.2.2 +mkdir src + +#Untar +tar -zxvf readline-6.2.2.tar.gz + +#Move readline into src directory +mv readline-6.2.2/* src +rm -rf readline-6.2.2 + +$install +cd src +python setup.py install Index: /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh (revision 12168) @@ -15,7 +15,7 @@ cd build ../source/configure \ - --prefix=$ISSM_TIER/externalpackages/rose/install \ - --with-boost=$ISSM_TIER/externalpackages/boost/install\ - --srcdir=$ISSM_TIER/externalpackages/rose/source + --prefix=$ISSM_DIR/externalpackages/rose/install \ + --with-boost=$ISSM_DIR/externalpackages/boost/install\ + --srcdir=$ISSM_DIR/externalpackages/rose/source if [ -z $1 ]; then Index: /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx64.sh (revision 12168) @@ -19,6 +19,6 @@ #install numpy cd numpy - python3.2 setup.py build - python3.2 setup.py install + python setup.py build + python setup.py install @@ -30,6 +30,6 @@ #install scipy cd scipy - python3.2 setup.py build - python3.2 setup.py install + python setup.py build + python setup.py install elif [[ $install == "3" ]];then Index: /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh (revision 12168) @@ -13,14 +13,14 @@ #Copy pcre prototype in include directory cd install -#cp $ISSM_TIER/externalpackages/pcre/install/pcre.h ./Source/Include/ -#cp $ISSM_TIER/externalpackages/pcre/install/.libs/* ./Source/Include/ -export CFLAGS="$CFLAGS -I$ISSM_TIER/externalpackages/pcre/install" -export LDFLAGS="-L$ISSM_TIER/externalpackages/pcre/install/.libs/" +#cp $ISSM_DIR/externalpackages/pcre/install/pcre.h ./Source/Include/ +#cp $ISSM_DIR/externalpackages/pcre/install/.libs/* ./Source/Include/ +export CFLAGS="$CFLAGS -I$ISSM_DIR/externalpackages/pcre/install" +export LDFLAGS="-L$ISSM_DIR/externalpackages/pcre/install/.libs/" export LIBS="-lpcre" #Configure doxygen ./configure \ - --prefix="$ISSM_TIER/externalpackages/python/install" \ - --with-pcre-prefix="$ISSM_TIER/externalpackages/pcre/install" \ - --with-pcre-exec-prefix="$ISSM_TIER/externalpackages/pcre/install" + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --with-pcre-prefix="$ISSM_DIR/externalpackages/pcre/install" \ + --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install" make make install Index: /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh (revision 12168) @@ -14,5 +14,5 @@ rm -rf tao-2.0-p3 cd install -export TAO_DIR="$ISSM_TIER/externalpackages/tao/install/" +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" #petsc needs to be compiled with --with-clanguage=C++ Index: sm/branches/trunk-jpl-damage/externalpackages/triangle/README =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/README (revision 12167) +++ (revision ) @@ -1,2 +1,0 @@ -Go pick up the correct configure.make file in the config directory (according to your platform), -copy it to the top triangle directory, and run install.sh Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/configs/android/android-4.0/configure.make =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/configs/android/android-4.0/configure.make (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/configs/android/android-4.0/configure.make (revision 12168) @@ -11,8 +11,8 @@ ANDROID_BIN=$(ISSM_TIER)/src/android/tmp/android-14-toolchain/bin -CC=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-gcc -AR=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ar -RANLIB=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ranlib -CSWITCHES = $(CFLAGS) -I/usr/X11R6/include -L/usr/X11R6/lib -I$(MATLAB_DIR)/extern/include -fPIC -I$(MATLAB_DIR)/include +CC=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc +AR=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ar +RANLIB=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib +CSWITCHES = $(CFLAGS) TRILIBDEFS = -DTRILIBRARY OBJ_EXT=o Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch.python =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch.python (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch.python (revision 12168) @@ -5,6 +5,6 @@ > * double precision activation in exactinit(); The rest is not changed. > * We also created the ice_makefile to compile Triangle into a library. */ -> #include -> #include +> /* #include +> #include */ > #define ANSI_DECLARATORS > #define NO_TIMER Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 12168) @@ -14,5 +14,5 @@ #configure cd install -./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" #Compile valgrind Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 12168) @@ -14,5 +14,5 @@ #configure cd install -./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" #Compile valgrind Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 12168) @@ -14,5 +14,5 @@ #configure cd install -./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only32bit +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only32bit #Compile valgrind Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 12168) @@ -14,5 +14,5 @@ #configure cd install -./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only64bit +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit #Compile valgrind Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 12168) @@ -14,5 +14,5 @@ #configure cd install -./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" #Compile valgrind Index: /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh (revision 12168) @@ -19,5 +19,5 @@ cd src/src ./configure \ - --prefix "$ISSM_TIER/externalpackages/vim/install" \ + --prefix "$ISSM_DIR/externalpackages/vim/install" \ --with-gcc "/usr/bin/gcc" Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12168) @@ -15,5 +15,5 @@ declare -x LOCALAPPDATA="C:\\Users\\schlegel\\AppData\\Local" declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" -declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/b/MATLAB/R2011b/bin:/cygdrive/c/MATLAB/R2011b/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" +declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2012a/runtime/win64:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/MATLAB/R2012a/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" declare -x PROCESSOR_ARCHITECTURE="x86" Index: /issm/branches/trunk-jpl-damage/m4/issm_options.m4 =================================================================== --- /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 12167) +++ /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 12168) @@ -13,31 +13,15 @@ fi dnl }}} - dnl Serial build {{{ - AC_ARG_WITH([serial], - AS_HELP_STRING([--with-serial = value],[serial compilation. ]), - [SERIAL_VALUE=$withval],[SERIAL_VALUE="yes"]) - AC_MSG_CHECKING(for serial compilation) - AM_CONDITIONAL([NOSERIAL], [test $SERIAL_VALUE = no]) - AM_CONDITIONAL([SERIAL], [test $SERIAL_VALUE = yes]) - AC_MSG_RESULT($SERIAL_VALUE) - dnl }}} - dnl Parallel build {{{ - AC_ARG_WITH([parallel], - AS_HELP_STRING([--with-parallel = value], [parallel compilation. ]), - [PARALLEL_VALUE=$withval],[PARALLEL_VALUE="yes"]) - AC_MSG_CHECKING(for parallel compilation) - AM_CONDITIONAL([NOPARALLEL], [test $PARALLEL_VALUE = no]) - AM_CONDITIONAL([PARALLEL], [test $PARALLEL_VALUE = yes]) - AC_MSG_RESULT($PARALLEL_VALUE) + dnl Modules build {{{ + AC_ARG_WITH([modules], + AS_HELP_STRING([--with-modules = value],[modules compilation. ]), + [MODULES_VALUE=$withval],[MODULES_VALUE="yes"]) + AC_MSG_CHECKING(for modules compilation) + AM_CONDITIONAL([MODULES], [test $MODULES_VALUE = yes]) + AC_MSG_RESULT($MODULES_VALUE) + dnl }}} + dnl Extensions{{{ ISSMEXT=".exe" AC_SUBST([ISSMEXT]) - dnl }}} - dnl Serial or Parallel check {{{ - dnl Check that at least serial or parallel builds have been requested! - if test "$SERIAL_VALUE" != "yes" ; then - if test "$PARALLEL_VALUE" != "yes"; then - AC_MSG_ERROR([cannot request --with-serial=no and --with-parallel=no at the same time!]) - fi - fi dnl }}} @@ -81,4 +65,8 @@ export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " + elif test $VENDOR = arm-linux; then + export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc + export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc + else AC_MSG_ERROR([unknow compiler vendor!]) @@ -92,8 +80,8 @@ dnl 1. See if matlab has been provided AC_ARG_WITH([matlab-dir], - AS_HELP_STRING([--with-matlab-dir = DIR], [matlab root directory. necessary for serial build.]), + AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]), [MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) - AC_MSG_CHECKING([wether Matlab is enabled]) + AC_MSG_CHECKING([whether matlab is enabled]) if test -d "$MATLAB_ROOT"; then HAVE_MATLAB=yes @@ -109,5 +97,5 @@ dnl 2. if matlab is provided, get version number if test x$HAVE_MATLAB = xyes; then - AC_MSG_CHECKING([for Matlab version]) + AC_MSG_CHECKING([for matlab version]) MATLAB_VERSION="" @@ -172,5 +160,5 @@ dnl 3. Get Matlab libraries - AC_MSG_CHECKING(for Matlab headers and libraries in $MATLAB_ROOT) + AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT) MATLABINCL=-I"$MATLAB_ROOT/extern/include"; @@ -191,9 +179,9 @@ *darwin*) dnl mex -v gives all the flags for compilation of mex files - dnl if matlab version is 7.10 or more, we must use mexmaci64 (64 bits) + dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits) MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" if test $MATLAB_MAJOR -ge 7; then - if test $MATLAB_MINOR -ge 10; then + if test $MATLAB_MINOR -ge 9; then MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++" @@ -217,6 +205,6 @@ AC_SUBST([MATLABINCL]) AC_SUBST([MEX]) - WRAPPEREXT=$MEXEXT - AC_SUBST([WRAPPEREXT]) + MATLABWRAPPEREXT=$MEXEXT + AC_SUBST([MATLABWRAPPEREXT]) AC_SUBST([MEXLIB]) AC_SUBST([MEXLINK]) @@ -225,7 +213,7 @@ dnl triangle {{{ AC_ARG_WITH([triangle-dir], - AS_HELP_STRING([--with-triangle-dir = DIR], [triangle root directory. necessary for serial build]), + AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]), [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT=""]) - AC_MSG_CHECKING(for Triangle headers and libraries) + AC_MSG_CHECKING(for triangle headers and libraries) if test -d "$TRIANGLE_ROOT"; then @@ -266,7 +254,7 @@ dnl dakota{{{ AC_ARG_WITH([dakota-dir], - AS_HELP_STRING([--with-dakota-dir = DIR], [dakota root directory. necessary for serial build]), + AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]), [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) - AC_MSG_CHECKING(for Dakota) + AC_MSG_CHECKING(for dakota) if test -d "$DAKOTA_ROOT"; then @@ -299,7 +287,7 @@ dnl boost{{{ AC_ARG_WITH([boost-dir], - AS_HELP_STRING([--with-boost-dir = DIR], [boost root directory.]), + AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]), [BOOST_ROOT=$withval],[BOOST_ROOT=""]) - AC_MSG_CHECKING(for Boost) + AC_MSG_CHECKING(for boost) if test -d "$BOOST_ROOT"; then @@ -318,9 +306,29 @@ AC_MSG_RESULT($HAVE_BOOST) dnl }}} + dnl python-version{{{ + AC_ARG_WITH([python-version], + AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), + [PYTHONVERSION=$withval],[PYTHONVERSION=""]) + AC_MSG_CHECKING(for python version) + + HAVE_PYTHON3="no" + + dnl recover major: + PYTHON_MAJOR=${PYTHONVERSION%.*} + + if test x$PYTHON_MAJOR = x3; then + dnl are we running python 3? + HAVE_PYTHON3="yes" + fi + AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) + + AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) + AC_MSG_RESULT($PYTHON_MAJOR) + dnl }}} dnl python{{{ AC_ARG_WITH([python-dir], - AS_HELP_STRING([--with-python-dir = DIR], [python root directory.]), + AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), [PYTHON_ROOT=$withval],[PYTHON_ROOT=""]) - AC_MSG_CHECKING(for Python) + AC_MSG_CHECKING(for python) if test -d "$PYTHON_ROOT"; then @@ -328,5 +336,5 @@ HAVE_PYTHON=yes PYTHONINCL=-I$PYTHON_ROOT/include - PYTHONLIB="-L$PYTHON_ROOT/lib -lpython3.2" + PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION" PYTHONEXT=.so PYTHONLINK="-dynamiclib" @@ -335,6 +343,6 @@ AC_SUBST([PYTHONINCL]) AC_SUBST([PYTHONLIB]) - WRAPPEREXT=$PYTHONEXT - AC_SUBST([WRAPPEREXT]) + PYTHONWRAPPEREXT=$PYTHONEXT + AC_SUBST([PYTHONWRAPPEREXT]) AC_SUBST([PYTHONLINK]) else @@ -346,7 +354,7 @@ dnl python-numpy{{{ AC_ARG_WITH([python-numpy-dir], - AS_HELP_STRING([--with-python-numpy-dir = DIR], [python-numpy root directory.]), + AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT=""]) - AC_MSG_CHECKING(for Python-Numpy) + AC_MSG_CHECKING(for python-numpy) if test -d "$PYTHON_NUMPY_ROOT"; then @@ -364,7 +372,7 @@ dnl chaco{{{ AC_ARG_WITH([chaco-dir], - AS_HELP_STRING([--with-chaco-dir = DIR], [chaco root directory.]), + AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]), [CHACO_ROOT=$withval],[CHACO_ROOT=""]) - AC_MSG_CHECKING(for Chaco) + AC_MSG_CHECKING(for chaco) if test -d "$CHACO_ROOT"; then @@ -386,7 +394,7 @@ dnl scotch{{{ AC_ARG_WITH([scotch-dir], - AS_HELP_STRING([--with-scotch-dir = DIR], [scotch root directory.]), + AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]), [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) - AC_MSG_CHECKING(for Scotch) + AC_MSG_CHECKING(for scotch) if test -d "$SCOTCH_ROOT"; then @@ -408,7 +416,7 @@ dnl adolc{{{ AC_ARG_WITH([adolc-dir], - AS_HELP_STRING([--with-adolc-dir = DIR], [adolc root directory.]), + AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]), [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) - AC_MSG_CHECKING(for ADOLC) + AC_MSG_CHECKING(for adolc) if test "x$ADOLC_ROOT" = "xno"; then @@ -436,7 +444,7 @@ dnl adic2{{{ AC_ARG_WITH([adic2-dir], - AS_HELP_STRING([--with-adic2-dir = DIR], [adic2 root directory.]), + AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]), [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) - AC_MSG_CHECKING(for ADIC2) + AC_MSG_CHECKING(for adic2) if test "x$ADIC2_ROOT" = "xno"; then @@ -464,7 +472,7 @@ dnl gsl{{{ AC_ARG_WITH([gsl-dir], - AS_HELP_STRING([--with-gsl-dir = DIR], [gsl root directory.]), + AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]), [GSL_ROOT=$withval],[GSL_ROOT=""]) - AC_MSG_CHECKING(for Gsl) + AC_MSG_CHECKING(for gsl) if test -d "$GSL_ROOT"; then @@ -487,7 +495,7 @@ dnl rose{{{ AC_ARG_WITH([rose-dir], - AS_HELP_STRING([--with-rose-dir = DIR], [rose root directory.]), + AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), [ROSE_ROOT=$withval],[ROSE_ROOT=""]) - AC_MSG_CHECKING(for Rose) + AC_MSG_CHECKING(for rose) if test -d "$ROSE_ROOT"; then @@ -510,10 +518,10 @@ dnl metis{{{ AC_ARG_WITH([metis-dir], - AS_HELP_STRING([--with-metis-dir = DIR],[metis root directory. necessary for serial build]), + AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]), [METIS_ROOT=$withval],[METIS_ROOT=""]) if test -d "$METIS_ROOT"; then - AC_MSG_CHECKING(for Metis headers and libraries in $METIS_ROOT) + AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) dnl first figure out version of metis: does the VERSION file exist? @@ -568,10 +576,5 @@ HAVE_METIS=no fi - - if test $HAVE_METIS = no; then - AC_MSG_ERROR([--with-metis-dir missing. Metis is needed to run ISSM]); - else - AC_MSG_RESULT($HAVE_METIS) - fi + AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) dnl }}} dnl mpi{{{ @@ -582,5 +585,5 @@ AC_ARG_WITH([mpi-include], - AS_HELP_STRING([--with-mpi-include = DIR],[mpi include directory, necessary for parallel build]), + AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]), [MPI_INCLUDE=$withval],[MPI_INCLUDE=""]) @@ -591,4 +594,5 @@ HAVE_MPI=no else + HAVE_MPI=yes MPIINCL=-I"$MPI_INCLUDE/" AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src]) @@ -598,13 +602,14 @@ fi fi - AC_MSG_RESULT(done) + AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes]) + AC_MSG_RESULT($HAVE_MPI) dnl }}} dnl petsc{{{ AC_ARG_WITH([petsc-dir], - AS_HELP_STRING([--with-petsc-dir = DIR],[PETSc root directory, necessary for parallel build]), + AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]), [PETSC_ROOT=$withval],[PETSC_ROOT=""]) if test -d "$PETSC_ROOT"; then - AC_MSG_CHECKING(for PETSc version) + AC_MSG_CHECKING(for petsc version) PETSC_MAJOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'` PETSC_MINOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MINOR" | sed 's/#define PETSC_VERSION_MINOR//' | sed 's/ //g'` @@ -614,5 +619,5 @@ PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' ` - AC_MSG_CHECKING(wether PETSc is the development version) + AC_MSG_CHECKING(whether petsc is the development version) if test x$PETSC_VERSION_DATE_HG = xunknown; then AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev]) @@ -624,8 +629,8 @@ AC_ARG_WITH([petsc-arch], - AS_HELP_STRING([--with-petsc-arch = DIR],[PETSc arch , necessary for parallel build]), + AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch , necessary for parallel build]), [PETSC_ARCH=$withval],[PETSC_ARCH=""]) - AC_MSG_CHECKING(for PETSc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) + AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) if test -d "$PETSC_ROOT"; then @@ -671,7 +676,7 @@ dnl tao{{{ AC_ARG_WITH([tao-dir], - AS_HELP_STRING([--with-tao-dir = DIR], [tao root directory.]), + AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]), [TAO_ROOT=$withval],[TAO_ROOT=""]) - AC_MSG_CHECKING(for Tao) + AC_MSG_CHECKING(for tao) if test -d "$TAO_ROOT"; then @@ -689,33 +694,10 @@ AC_MSG_RESULT($HAVE_TAO) dnl }}} - dnl mpiuni{{{ - dnl when running in serial mode, MPI must be ignored, and set to internal petsc mpiuni: - if test "$PARALLEL_VALUE" = "no" ; then - HAVE_MPI=yes - MPIINCL=-I"$PETSC_ROOT/include/mpiuni" - - case "${host_os}" in - *cygwin*) - dnl MPILIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libmpiuni.lib" - ;; - *linux*) - MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni" - ;; - *darwin*) - MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni" - ;; - esac - - AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src]) - AC_SUBST([MPIINCL]) - AC_SUBST([MPILIB]) - fi - dnl }}} dnl slepc{{{ AC_ARG_WITH([slepc-dir], - AS_HELP_STRING([--with-slepc-dir = DIR],[slepc root directory]), + AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]), [SLEPC_ROOT=$withval],[SLEPC_ROOT=""]) - AC_MSG_CHECKING(for Slepc headers and libraries in $SLEPC_ROOT) + AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT) if test -d "$SLEPC_ROOT"; then HAVE_SLEPC=yes @@ -733,8 +715,8 @@ dnl shapelib{{{ AC_ARG_WITH([shapelib-dir], - AS_HELP_STRING([--with-shapelib-dir = DIR], [shapelib root directory]), + AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]), [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT=""]) - AC_MSG_CHECKING(for Shapelib headers and libraries in $SHAPELIB_ROOT) + AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT) if test -d "$SHAPELIB_ROOT"; then @@ -754,8 +736,8 @@ dnl scalapack{{{ AC_ARG_WITH([scalapack-dir], - AS_HELP_STRING([--with-scalapack-dir = DIR],[scalapack root directory]), + AS_HELP_STRING([--with-scalapack-dir=DIR],[scalapack root directory]), [SCALAPACK_ROOT=$withval],[SCALAPACK_ROOT=""]) - AC_MSG_CHECKING(for Scalapack headers and libraries in $SCALAPACK_ROOT) + AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT) if test -d "$SCALAPACK_ROOT"; then @@ -773,8 +755,8 @@ dnl blas{{{ AC_ARG_WITH([blas-lapack-dir], - AS_HELP_STRING([--with-blas-lapack-dir = DIR],[blas-lapack root directory]), + AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]), [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT=""]) - AC_MSG_CHECKING(for Blas and Lapack headers and libraries in $BLASLAPACK_ROOT) + AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT) if test -d "$BLASLAPACK_ROOT"; then @@ -806,5 +788,5 @@ dnl mkl{{{ AC_ARG_WITH([mkl-dir], - AS_HELP_STRING([--with-mkl-dir = DIR],[mkl root directory]), + AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]), [MKL_ROOT=$withval],[MKL_ROOT=""]) @@ -825,8 +807,9 @@ dnl }}} dnl plapack{{{ + AC_MSG_CHECKING(for plapack) + AC_ARG_WITH([plapack-lib], AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]), [PLAPACK_LIB=$withval],[PLAPACK_LIB=""]) - AC_MSG_CHECKING(for Plapack libraries) AC_ARG_WITH([plapack-include], @@ -834,5 +817,4 @@ [plapack include ]), [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""]) - AC_MSG_CHECKING(for Plapack headers) if test -n "$PLAPACK_LIB"; then @@ -857,8 +839,8 @@ dnl mumps{{{ AC_ARG_WITH([mumps-dir], - AS_HELP_STRING([--with-mumps-dir = DIR],[mumps root directory]), + AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]), [MUMPS_ROOT=$withval],[MUMPS_ROOT=""]) - AC_MSG_CHECKING(for Mumps headers and libraries in $MUMPS_ROOT) + AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT) if test -d "$MUMPS_ROOT"; then @@ -882,8 +864,8 @@ dnl blacs{{{ AC_ARG_WITH([blacs-dir], - AS_HELP_STRING([--with-blacs-dir = DIR],[blacs root directory]), + AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]), [BLACS_ROOT=$withval],[BLACS_ROOT=""]) - AC_MSG_CHECKING(for Blacs headers and libraries in $BLACS_ROOT) + AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT) if test -d "$BLACS_ROOT"; then @@ -903,8 +885,8 @@ dnl hypre{{{ AC_ARG_WITH([hypre-dir], - AS_HELP_STRING([--with-hypre-dir = DIR],[hypre root directory]), + AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]), [HYPRE_ROOT=$withval],[HYPRE_ROOT=""]) - AC_MSG_CHECKING(for Hypre headers and libraries in $HYPRE_ROOT) + AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT) if test -d "$HYPRE_ROOT"; then @@ -924,8 +906,8 @@ dnl ml{{{ AC_ARG_WITH([ml-dir], - AS_HELP_STRING([--with-ml-dir = DIR],[ml root directory]), + AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]), [ML_ROOT=$withval],[ML_ROOT=""]) - AC_MSG_CHECKING(for Ml headers and libraries in $ML_ROOT) + AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT) if test -d "$ML_ROOT"; then @@ -1229,5 +1211,5 @@ AC_MSG_CHECKING(consistency between all libraries) - dnl check that if petsc is requested in parallel, mpi should be specified + dnl check that if petsc is requested , mpi should be specified if test "$HAVE_PETSC" = "yes" ; then if test "$HAVE_MPI" = "NO"; then @@ -1236,15 +1218,22 @@ fi - dnl check that we have either python or matlab support if we only compile serially - if test "$PARALLEL_VALUE" = "no" && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then - AC_MSG_ERROR([need at least python or matlab support to compile only in serial mode!]); - fi - - dnl check that we don't have with-matlab and with-python at the same time - if test "$HAVE_PYTHON" = "yes" ; then - if test "$HAVE_MATLAB" = "yes"; then - AC_MSG_ERROR([cannot create matlab and python wrappers simultaneously! Please choose one or the other.]); - fi - fi + dnl check that we have either python or matlab support if we compile the modules + if test "$MODULES_VALUE" = "yes" && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then + AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]); + fi + + dnl check that we have python version if python compile is specified + if test "$HAVE_PYTHON" = "yes" && test "$PYTHONVERSION" = "" ; then + AC_MSG_ERROR([need python-version if python compile is required!]); + fi + + dnl check that if we have MPI, we have metis + if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then + AC_MSG_ERROR([need mpi if using the metis partitioner!]); + fi + + + + AC_MSG_RESULT(done) @@ -1257,5 +1246,5 @@ AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]), [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) - AC_MSG_CHECKING(for C++ optimization flags) + AC_MSG_CHECKING(for c++ optimization flags) AC_SUBST([CXXOPTFLAGS]) AC_MSG_RESULT(done) Index: /issm/branches/trunk-jpl-damage/scripts/GenerateReferences.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/GenerateReferences.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/GenerateReferences.sh (revision 12168) @@ -16,5 +16,5 @@ \begin{document} \nocite{$CITE} -\bibliography{$ISSM_DIR/publications/bibtex/references} +\bibliography{$JPL_SVN/publications/bibtex/references} \end{document} END @@ -29,5 +29,5 @@ mv references.bak2 references.bbl echo "Converting to rtf" -$ISSM_TIER/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_TIER/externalpackages/latex2rtf/install/cfg/ references +$ISSM_DIR/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_DIR/externalpackages/latex2rtf/install/cfg/ references #Remove all but rtf file Index: /issm/branches/trunk-jpl-damage/scripts/archive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/archive.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/archive.sh (revision 12168) @@ -10,5 +10,5 @@ #Cleanup code -cd $ISSM_TIER +cd $ISSM_DIR make clean make distclean @@ -18,5 +18,5 @@ #Create tar file, with today's date in the title; -cd $ISSM_TIER/.. +cd $ISSM_DIR/.. today=`today_date` -tar zcvf issm-3.0-$today.tar.gz `basename $ISSM_TIER` +tar zcvf issm-3.0-$today.tar.gz `basename $ISSM_DIR` Index: /issm/branches/trunk-jpl-damage/scripts/automakererun.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/automakererun.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/automakererun.sh (revision 12168) @@ -4,8 +4,8 @@ - ACLOCAL="$ISSM_TIER/externalpackages/automake/install/bin/aclocal" -AUTOCONF="$ISSM_TIER/externalpackages/autoconf/install/bin/autoconf" -AUTOHEAD="$ISSM_TIER/externalpackages/autoconf/install/bin/autoheader" -AUTOMAKE="$ISSM_TIER/externalpackages/automake/install/bin/automake" + ACLOCAL="$ISSM_DIR/externalpackages/automake/install/bin/aclocal" +AUTOCONF="$ISSM_DIR/externalpackages/autoconf/install/bin/autoconf" +AUTOHEAD="$ISSM_DIR/externalpackages/autoconf/install/bin/autoheader" +AUTOMAKE="$ISSM_DIR/externalpackages/automake/install/bin/automake" echo "removing config.cach" Index: /issm/branches/trunk-jpl-damage/scripts/cloc2html.py =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/cloc2html.py (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/cloc2html.py (revision 12168) @@ -4,6 +4,6 @@ import sys, re, os -ISSM_TIER=os.getenv('ISSM_TIER'); -if(not ISSM_TIER): raise NameError('ISSM_TIER undefined') +ISSM_DIR=os.getenv('ISSM_DIR'); +if(not ISSM_DIR): raise NameError('ISSM_DIR undefined') infile = open('temp','r') Index: /issm/branches/trunk-jpl-damage/scripts/convertmatlabclasses.py =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/convertmatlabclasses.py (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/convertmatlabclasses.py (revision 12168) @@ -4,8 +4,8 @@ #get names of all directories to process -ISSM_TIER=os.getenv('ISSM_TIER'); -if(not ISSM_TIER): raise NameError('ISSM_TIER undefined') -newclassesdir = ISSM_TIER + '/src/m/classes/' -oldclassesdir = ISSM_TIER + '/src/m/oldclasses/' +ISSM_DIR=os.getenv('ISSM_DIR'); +if(not ISSM_DIR): raise NameError('ISSM_DIR undefined') +newclassesdir = ISSM_DIR + '/src/m/classes/' +oldclassesdir = ISSM_DIR + '/src/m/oldclasses/' #make new directory Index: /issm/branches/trunk-jpl-damage/scripts/dailyrun.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/dailyrun.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/dailyrun.sh (revision 12168) @@ -54,15 +54,15 @@ #Prepare run #Windows hack for startup.m {{{1 -#windows environments: ISSM_TIER_WIN variable not correctly picked up when using -#the cron job. just get startup to take the ISSM_TIER variable as the pwd: +#windows environments: ISSM_DIR_WIN variable not correctly picked up when using +#the cron job. just get startup to take the ISSM_DIR variable as the pwd: if [ "$OS" = "winxp32" ] then - cat startup.m | sed 's/clear status/clear status; ISSM_TIER=pwd;/g' > startup.m.bak + cat startup.m | sed 's/clear status/clear status; ISSM_DIR=pwd;/g' > startup.m.bak mv startup.m.bak startup.m fi #}}} #create softlink to startup {{{1 -cd $ISSM_TIER/test/NightlyRun/ -ln -s $ISSM_TIER/startup.m . +cd $ISSM_DIR/test/NightlyRun/ +ln -s $ISSM_DIR/startup.m . #}}} #Create dailylog directory and info.log {{{1 @@ -70,7 +70,7 @@ INSTALL_TIME=$(timer) ELAPSED_INSTALL=$(timer $START_TIME) -rm -rf $ISSM_TIER/dailylog -mkdir $ISSM_TIER/dailylog -cat << END > $ISSM_TIER/dailylog/info.log +rm -rf $ISSM_DIR/dailylog +mkdir $ISSM_DIR/dailylog +cat << END > $ISSM_DIR/dailylog/info.log today: $(echo $TODAY) user: $(echo $USER) @@ -95,8 +95,8 @@ do #Launch matlab and the daily run script - cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF + cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF warning off %necessary to avoid a info.log of several Go for parallel runs try, - cd $ISSM_TIER/test/NightlyRun + cd $ISSM_DIR/test/NightlyRun startup; $(if [ "$NROPTIONS" = "" ] @@ -111,5 +111,5 @@ directory=strsplit(pwd,'/'); message=getReport(me) - fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); fprintf(fid,'%s',message); @@ -121,5 +121,5 @@ #Start run from dailylog directory - cd $ISSM_TIER/dailylog/ + cd $ISSM_DIR/dailylog/ #Start test @@ -132,5 +132,5 @@ #}}} #concatenate all reports {{{1 -cd $ISSM_TIER/dailylog/ +cd $ISSM_DIR/dailylog/ mv matlab_log1.log matlab_log.log for (( i=2;i<=$NUMCPUS_RUN;i++ )) @@ -149,5 +149,5 @@ ELAPSED_RUN=$(timer $INSTALL_TIME) ELAPSED_TOTAL=$(timer $START_TIME) -cat << END >> $ISSM_TIER/dailylog/info.log +cat << END >> $ISSM_DIR/dailylog/info.log elapsed_run: $(echo $ELAPSED_RUN) elapsed_total: $(echo $ELAPSED_TOTAL) @@ -158,7 +158,7 @@ #Send Report #Build html report {{{1 -cd $ISSM_TIER/dailylog/ +cd $ISSM_DIR/dailylog/ sh ../scripts/report.sh -ln -s $ISSM_TIER/dailylog/report.html $INIT_PATH -echo "html report located in $ISSM_TIER/dailylog/report.html and $INIT_PATH/report.html" +ln -s $ISSM_DIR/dailylog/report.html $INIT_PATH +echo "html report located in $ISSM_DIR/dailylog/report.html and $INIT_PATH/report.html" #}}} Index: /issm/branches/trunk-jpl-damage/scripts/getloc.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/getloc.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/getloc.sh (revision 12168) @@ -1,12 +1,12 @@ #!/bin/bash #get number of lines of code -cloc-1.55.pl $ISSM_TIER/src $ISSM_TIER/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp +cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp cat temp ./cloc2html.py rm temp -cat $ISSM_TIER/src/dox/issm.dox | sed '/ input1 -cat $ISSM_TIER/src/dox/issm.dox | sed '1,/<\/table>/d' > input2 -cat input1 temp.html input2 > $ISSM_TIER/src/dox/issm.dox +cat $ISSM_DIR/src/dox/issm.dox | sed '/
input1 +cat $ISSM_DIR/src/dox/issm.dox | sed '1,/<\/table>/d' > input2 +cat input1 temp.html input2 > $ISSM_DIR/src/dox/issm.dox rm input1 input2 temp.html @@ -19,10 +19,10 @@ #OLDER MANUAL VESION #get Matlab number of lines -cd $ISSM_TIER/src/m +cd $ISSM_DIR/src/m M_LOC=$(find . -name "*.m" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}'); echo "Matlab code: $M_LOC" #get C/CPP number of lines -cd $ISSM_TIER/src +cd $ISSM_DIR/src CPP_LOC=$(find . -name "*.cpp" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}'); echo "C++ code: $CPP_LOC" Index: /issm/branches/trunk-jpl-damage/scripts/issmconfiguration.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/issmconfiguration.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/issmconfiguration.sh (revision 12168) @@ -7,6 +7,6 @@ presendir=`pwd` -if test -d "$ISSM_TIER/configs" ; then - cd $ISSM_TIER/configs +if test -d "$ISSM_DIR/configs" ; then + cd $ISSM_DIR/configs LIST=`ls` @@ -40,5 +40,5 @@ echo "" - cd $ISSM_TIER + cd $ISSM_DIR source ./scripts/automakererun.sh source configs/$configurename @@ -56,3 +56,3 @@ -#alias aut='a=`pwd` && cd $ISSM_TIER && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh' +#alias aut='a=`pwd` && cd $ISSM_DIR && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh' Index: /issm/branches/trunk-jpl-damage/scripts/mail =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/mail (revision 12168) +++ /issm/branches/trunk-jpl-damage/scripts/mail (revision 12168) @@ -0,0 +1,158 @@ +#!/bin/sh + +# This is a shell script to emulate the standard mail(1) aka mailx(1) +# aka Mail(1) tool usage for sending emails. This shell script is not +# a client for checking or reading mail. Also, this version of mail +# does not touch any mail boxes. + +# Copyright (c) 2003 by Jeremy C. Reed +# This software is provided "as is" without any warranties. You may +# redistribute and use this source, with or without modification, +# as long as you include this copyright and disclaimer. + +# To do: some switches to consider: +# -v display details of delivery +# -E do not send empty messages +# -c send carbon copies to users +# -b send blind carbon copies + +# todo: test if read can read in long enough lines +# some shells may have limit of 256 characters per read? + +SENDMAIL=sendmail # set to path of your sendmail(8) command +SENDMAIL_ARGS="-t -i" # -i is so dot doesn't terminate message + # -t is to get recipients from headers + +unset subject +unset to_addr +dontsendempty=0 + +about () +{ + echo "This is mailx.sh version 0.03. This is simple, shell script" + echo "to implement mailx(1) functionality for sending mail. It does" + echo "not provide an interface for checking or reading email messages." + echo + + # maybe do this without forking a command + mailname=$( basename $0 ) + + if [ -n "$1" ] ; then + echo "$mailname: $1" 1>&2 + fi + + echo "Usage: $mailname [-s subject] to-addr ..." 1>&2 + + if [ -n "$1" ] ; then + if [ -n "$2" ] ; then + exit $2 + fi + exit 100 + fi + + exit 0 +} + +if [ $# -eq 0 ] ; then + about "Sorry, this is not a mail reader." 1 +fi + +while [ -n "$1" ] ; do + case "$1" in + -*) + if [ "$1" = "-s" ] ; then + if [ -z "$2" ] ; then + about "The \"-s\" option requires an argument." 4 + fi + subject="$2" + shift + elif [ "$1" = "-u" -o "$1" = "-f" ] ; then + about "Sorry, this is not a mail reader." 2 +# elif [ "$1" = "-E" ] ; then +# this probably needs to have entire message saved to temp file first +# dontsendempty=1 + else +# about "unknown option -- $1" 3 + about "Switch \"$1\" is not implemented." 3 + fi + ;; + *) if [ -n "$to_addr" ] ; then + to_addr="${to_addr}, $1" + else + to_addr="$1" + fi + ;; + esac + shift +done + + +if [ -t 0 ] ; then # no piped in standard input + if [ -z "$subject" ] ; then + echo -n "Subject: " + OLD_IFS=$IFS + IFS="" + read -r subject + IFS=$OLD_IFS + fi +fi + +if [ -z "$to_addr" ] ; then + about "No recipients specified." 6 +# about "You must specify recipients." 6 +fi + +# generate SMTP headers + +# mail(1) doesn't seem to set date +#date +"Date: %a, %e %b %G %T %z" +## maybe pipe though sed to get rid of extra space +## before single digit day of month? + +{ +# if [ -n "$to_addr" ] ; then +echo "To: ${to_addr}" +# fi + +if [ -n "$subject" ] ; then + echo "Subject: $subject" +fi + +# end of headers +echo "" + +# output +line_count=0 +OLD_IFS=$IFS +IFS="" +while read -r line ; do + # finish if manual, non-piped input is a period on a line by itself + if [ "$line" = "." -a -t 0 ] ; then + break + fi + echo "$line" + line_count=$(( line_count + 1 )) +done + +IFS=$OLD_IFS + +if [ -t 0 ] ; then # no piped in standard input + echo "EOT" 1>&2 +fi + +# later add switch to not send mail by exiting +if [ "$line_count" -eq 0 ] ; then +# if [ "$dontsendempty" -eq 1 ] ; then +# todo this, have it save to temp file and then send to sendmail as needed +# # No message, so just exit cleanly +# exit 0 +# fi + if [ -z "$subject" ] ; then + echo "No message, no subject; hope that's ok" 1>&2 + else + echo "Null message body; hope that's ok" 1>&2 + fi +fi + +} | $SENDMAIL $SENDMAIL_ARGS + Index: /issm/branches/trunk-jpl-damage/scripts/report.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/report.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/report.sh (revision 12168) @@ -49,5 +49,5 @@ #create some variables -if [ $(ls -1 $ISSM_TIER/bin | wc -l) -le 20 ]; +if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ]; then IS_INSTALL=0 Index: /issm/branches/trunk-jpl-damage/scripts/run.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/run.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/run.sh (revision 12168) @@ -6,6 +6,6 @@ MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8 #create softlink to startup {{{1 -cd $ISSM_TIER/test/NightlyRun/ -ln -s $ISSM_TIER/startup.m . +cd $ISSM_DIR/test/NightlyRun/ +ln -s $ISSM_DIR/startup.m . #}}} @@ -14,8 +14,8 @@ do #Launch matlab and the daily run script - cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF + cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF warning off %necessary to avoid a daily.log of several Go for parallel runs try, - cd $ISSM_TIER/test/NightlyRun + cd $ISSM_DIR/test/NightlyRun startup; $(if [ "$NROPTIONS" = "" ] @@ -30,5 +30,5 @@ directory=strsplit(pwd,'/'); message=getReport(me) - fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); fprintf(fid,'%s',message); @@ -39,5 +39,5 @@ #Start run from dailylog directory - cd $ISSM_TIER/dailylog/ + cd $ISSM_DIR/dailylog/ #Start test Index: /issm/branches/trunk-jpl-damage/scripts/windowsbuild.sh =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/windowsbuild.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/scripts/windowsbuild.sh (revision 12168) @@ -11,5 +11,5 @@ today=`today_date` -cd $ISSM_TIER/bin +cd $ISSM_DIR/bin #Filter out .svn files Index: /issm/branches/trunk-jpl-damage/src/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/Makefile.am (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/Makefile.am (revision 12168) @@ -1,2 +1,2 @@ -EXTRA_DIST = perl pro -SUBDIRS = c mex m +EXTRA_DIST = perl pro +SUBDIRS = c modules m py Index: /issm/branches/trunk-jpl-damage/src/c/Container/Constraints.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Constraints.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Constraints.cpp (revision 12168) @@ -48,10 +48,11 @@ /*figure out total number of constraints combining all the cpus (no clones here)*/ - #ifdef _PARALLEL_ - MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); - MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); #else - numberofconstraints=localconstraints; + numberofconstraints=localconstraints; #endif + return numberofconstraints; Index: /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.cpp (revision 12168) @@ -84,329 +84,4 @@ /*}}}*/ -/*I/O*/ -#ifdef _SERIAL_ -/*FUNCTION DataSet::Marshall{{{1*/ -char* DataSet::Marshall(){ - - vector::iterator object; - int object_size; - int marshalled_dataset_size=0; - char* marshalled_dataset=NULL; - char* old_marshalled_dataset=NULL; - - /*First get size of marshalled dataset: */ - object_size=(int)objects.size(); - - marshalled_dataset_size=MarshallSize(); - - /*Allocate marshalled dataset: */ - marshalled_dataset=(char*)xmalloc(marshalled_dataset_size*sizeof(char)); - - /*Keep track of old_marshalled_dataset: */ - old_marshalled_dataset=marshalled_dataset; - - /*Store internals of dataset first: */ - memcpy(marshalled_dataset,&object_size,sizeof(int)); marshalled_dataset+=sizeof(int); - memcpy(marshalled_dataset,&sorted,sizeof(int)); marshalled_dataset+=sizeof(int); - if(sorted){ - if(object_size)memcpy(marshalled_dataset,sorted_ids,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); - if(object_size)memcpy(marshalled_dataset,id_offsets,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); - } - - for ( object=objects.begin() ; object < objects.end(); object++ ){ - (*object)->Marshall(&marshalled_dataset); - } - - /* Ok, marshalled_dataset now points to the end of the original marshalled_dataset pointer - * before we started the loop on objects. Get object to point right again: */ - marshalled_dataset-=marshalled_dataset_size; - - /*We should be back to old_marshalled_dataset: check and abort if that's not the case, - * because this is a nasty error: */ - if (marshalled_dataset!=old_marshalled_dataset){ - _error_("final marshalled dataset \"%s\" is different from initial one!",EnumToStringx(enum_type)); - abort(); - } - - /*Return: */ - return marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DataSet::MarshallSize{{{1*/ -int DataSet::MarshallSize(){ - - vector::iterator object; - int marshalled_dataset_size=0; - - - for ( object=objects.begin() ; object < objects.end(); object++ ){ - marshalled_dataset_size+= (*object)->MarshallSize(); - } - - marshalled_dataset_size+=sizeof(int); //objects size - marshalled_dataset_size+=sizeof(int); //sorted size - if(sorted){ - marshalled_dataset_size+=(int)objects.size()*sizeof(int); //sorted ids - marshalled_dataset_size+=(int)objects.size()*sizeof(int); //id offsets - } - - return marshalled_dataset_size; -} -/*}}}*/ -/*FUNCTION DataSet::Demarshall{{{1*/ -DataSet* DataSetDemarshall(char* marshalled_dataset){ - - return DataSetDemarshallRaw(&marshalled_dataset); - -} -/*}}}*/ -/*FUNCTION DataSet::DemarshallRaw{{{1*/ -DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset){ - - int i; - - DataSet* dataset=NULL; - int numobjects=0; - int enum_type; - Object* object=NULL; - int sorted; - int* sorted_ids=NULL; - int* id_offsets=NULL; - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset pointer: */ - marshalled_dataset=*pmarshalled_dataset; - - /*initialize dataset: */ - dataset=new DataSet(); - - /*Get internals first: */ - memcpy(&numobjects,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - memcpy(&sorted,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(sorted){ - if(numobjects){ - sorted_ids=(int*)xmalloc(numobjects*sizeof(int)); - id_offsets=(int*)xmalloc(numobjects*sizeof(int)); - memcpy(sorted_ids,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); - memcpy(id_offsets,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); - } - dataset->SetSorting(sorted_ids,id_offsets); - } - - for(i=0;iDemarshall(&marshalled_dataset); - dataset->AddObject(node);} - break; - case VertexEnum:{ - Vertex* vertex=NULL; - vertex=new Vertex(); - vertex->Demarshall(&marshalled_dataset); - dataset->AddObject(vertex);} - break; - case DoubleParamEnum:{ - DoubleParam* doubleparam=NULL; - doubleparam=new DoubleParam(); - doubleparam->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleparam);} - break; - case TriaEnum:{ - Tria* tria=NULL; - tria=new Tria(); - tria->Demarshall(&marshalled_dataset); - dataset->AddObject(tria);} - break; - case TriaP1InputEnum:{ - TriaP1Input* triavertexinput=NULL; - triavertexinput=new TriaP1Input(); - triavertexinput->Demarshall(&marshalled_dataset); - dataset->AddObject(triavertexinput);} - break; - #ifdef _HAVE_3D_ - case PentaP1InputEnum:{ - PentaP1Input* pentavertexinput=NULL; - pentavertexinput=new PentaP1Input(); - pentavertexinput->Demarshall(&marshalled_dataset); - dataset->AddObject(pentavertexinput);} - break; - #endif - case TransientInputEnum:{ - TransientInput* transientinput=NULL; - transientinput=new TransientInput(); - transientinput->Demarshall(&marshalled_dataset); - dataset->AddObject(transientinput);} - break; - #ifdef _HAVE_CONTROL_ - case ControlInputEnum:{ - ControlInput* controlinputinput=NULL; - controlinputinput=new ControlInput(); - controlinputinput->Demarshall(&marshalled_dataset); - dataset->AddObject(controlinputinput);} - break; - #endif - case DatasetInputEnum:{ - DatasetInput* datasetinputinput=NULL; - datasetinputinput=new DatasetInput(); - datasetinputinput->Demarshall(&marshalled_dataset); - dataset->AddObject(datasetinputinput);} - break; - case TriaP1ElementResultEnum:{ - TriaP1ElementResult* triavertexelementresult=NULL; - triavertexelementresult=new TriaP1ElementResult(); - triavertexelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(triavertexelementresult);} - break; - #ifdef _HAVE_3D_ - case PentaP1ElementResultEnum:{ - PentaP1ElementResult* pentavertexelementresult=NULL; - pentavertexelementresult=new PentaP1ElementResult(); - pentavertexelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(pentavertexelementresult);} - break; - case PentaEnum:{ - Penta* penta=NULL; - penta=new Penta(); - penta->Demarshall(&marshalled_dataset); - dataset->AddObject(penta);} - break; - #endif - case MaticeEnum:{ - Matice* matice=NULL; - matice=new Matice(); - matice->Demarshall(&marshalled_dataset); - dataset->AddObject(matice);} - break; - case MatparEnum:{ - Matpar* matpar=NULL; - matpar=new Matpar(); - matpar->Demarshall(&marshalled_dataset); - dataset->AddObject(matpar);} - break; - case SpcStaticEnum:{ - SpcStatic* spcstatic=NULL; - spcstatic=new SpcStatic(); - spcstatic->Demarshall(&marshalled_dataset); - dataset->AddObject(spcstatic);} - break; - case SpcDynamicEnum:{ - SpcDynamic* spcdynamic=NULL; - spcdynamic=new SpcDynamic(); - spcdynamic->Demarshall(&marshalled_dataset); - dataset->AddObject(spcdynamic);} - break; - case SpcTransientEnum:{ - SpcTransient* spctransient=NULL; - spctransient=new SpcTransient(); - spctransient->Demarshall(&marshalled_dataset); - dataset->AddObject(spctransient);} - break; - case PengridEnum:{ - Pengrid* pengrid=NULL; - pengrid=new Pengrid(); - pengrid->Demarshall(&marshalled_dataset); - dataset->AddObject(pengrid);} - break; - case PenpairEnum:{ - Penpair* penpair=NULL; - penpair=new Penpair(); - penpair->Demarshall(&marshalled_dataset); - dataset->AddObject(penpair);} - break; - case IcefrontEnum:{ - Icefront* icefront=NULL; - icefront=new Icefront(); - icefront->Demarshall(&marshalled_dataset); - dataset->AddObject(icefront);} - break; - case NumericalfluxEnum:{ - Numericalflux* numericalflux=NULL; - numericalflux=new Numericalflux(); - numericalflux->Demarshall(&marshalled_dataset); - dataset->AddObject(numericalflux);} - break; - #ifdef _HAVE_RIFTS_ - case RiftfrontEnum:{ - Riftfront* riftfront=NULL; - riftfront=new Riftfront(); - riftfront->Demarshall(&marshalled_dataset); - dataset->AddObject(riftfront);} - break; - #endif - case DoubleInputEnum:{ - DoubleInput* doubleinput=NULL; - doubleinput=new DoubleInput(); - doubleinput->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleinput);} - break; - case IntInputEnum:{ - IntInput* intinput=NULL; - intinput=new IntInput(); - intinput->Demarshall(&marshalled_dataset); - dataset->AddObject(intinput);} - break; - case BoolInputEnum:{ - BoolInput* boolinput=NULL; - boolinput=new BoolInput(); - boolinput->Demarshall(&marshalled_dataset); - dataset->AddObject(boolinput);} - break; - case IntParamEnum:{ - IntParam* intparam=NULL; - intparam=new IntParam(); - intparam->Demarshall(&marshalled_dataset); - dataset->AddObject(intparam);} - break; - case BoolParamEnum:{ - BoolParam* boolparam=NULL; - boolparam=new BoolParam(); - boolparam->Demarshall(&marshalled_dataset); - dataset->AddObject(boolparam);} - break; - case StringParamEnum:{ - StringParam* stringparam=NULL; - stringparam=new StringParam(); - stringparam->Demarshall(&marshalled_dataset); - dataset->AddObject(stringparam);} - break; - case DoubleVecExternalResultEnum:{ - DoubleVecExternalResult* doublevecexternalresult=NULL; - doublevecexternalresult=new DoubleVecExternalResult(); - doublevecexternalresult->Demarshall(&marshalled_dataset); - dataset->AddObject(doublevecexternalresult);} - break; - case DoubleExternalResultEnum:{ - DoubleExternalResult* doubleexternalresult=NULL; - doubleexternalresult=new DoubleExternalResult(); - doubleexternalresult->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleexternalresult);} - break; - #ifdef _HAVE_GROUNDINGLINE_ - case BoolElementResultEnum:{ - BoolElementResult* boolelementresult=NULL; - boolelementresult=new BoolElementResult(); - boolelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(boolelementresult);} - break; - #endif - default: - _error_("could not recognize enum type: %s",EnumToStringx(enum_type)); - } - } - - /*Assign output pointers:*/ - *pmarshalled_dataset=marshalled_dataset; - - return dataset; -} -/*}}}*/ -#endif - /*Specific methods*/ /*FUNCTION DataSet::AddObject{{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/DataSet.h (revision 12168) @@ -49,8 +49,4 @@ void Echo(); void DeepEcho(); - #ifdef _SERIAL_ - char* Marshall(); - int MarshallSize(); - #endif int AddObject(Object* object); int DeleteObject(int id); @@ -69,11 +65,3 @@ }; -/*This routine cannot be object oriented, but need for demarshalling: */ -#ifdef _SERIAL_ -DataSet* DataSetDemarshall(char* marshalled_dataset); -DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset); #endif - - - -#endif Index: /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp (revision 12168) @@ -124,6 +124,6 @@ } - #ifdef _PARALLEL_ /*Synchronize across cluster, so as to not end up with different sizes for each patch on each cpu: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&numvertices,&max_numvertices,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&max_numvertices,1,MPI_INT,0,MPI_COMM_WORLD); @@ -193,7 +193,11 @@ /*Get rank of first cpu that has results*/ + #ifdef _HAVE_MPI_ if(this->Size()) rank=my_rank; else rank=num_procs; MPI_Allreduce (&rank,&minrank,1,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + minrank=my_rank; + #endif /*see what the first element of this partition has in stock (this is common to all partitions)*/ @@ -203,8 +207,11 @@ element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numberofresults,1,MPI_DOUBLE,minrank,MPI_COMM_WORLD); + #endif /*Get out if there is no results. Otherwise broadcast info*/ if(!numberofresults) return; + #ifdef _HAVE_MPI_ if(my_rank!=minrank){ resultsenums=(int*)xmalloc(numberofresults*sizeof(int)); @@ -217,4 +224,5 @@ MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,minrank,MPI_COMM_WORLD); MPI_Bcast(resultssteps,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); + #endif /*Loop over all results and get nodal vector*/ @@ -250,7 +258,5 @@ /*Gather onto master cpu 0, if needed: */ -#ifdef _PARALLEL_ if(io_gather)patch->Gather(); -#endif /*create result object and add to results dataset:*/ @@ -276,9 +282,9 @@ int numberofelements; - #ifdef _PARALLEL_ local_nelem=this->Size(); + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&local_nelem,(void*)&numberofelements,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); #else - numberofelements=this->Size(); + numberofelements=local_nelem; #endif Index: /issm/branches/trunk-jpl-damage/src/c/Container/Loads.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Loads.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Loads.cpp (revision 12168) @@ -63,5 +63,5 @@ /*figure out total number of loads combining all the cpus (no clones here)*/ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce(&localloads,&numberofloads,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&numberofloads,1,MPI_INT,0,MPI_COMM_WORLD); @@ -69,4 +69,5 @@ numberofloads=localloads; #endif + return numberofloads; Index: /issm/branches/trunk-jpl-damage/src/c/Container/Nodes.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Nodes.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Nodes.cpp (revision 12168) @@ -83,8 +83,12 @@ * 0. This means the dofs between all the cpus are not unique. We now offset the dofs of eache * cpus by the total last dofs of the previus cpu, starting from 0. - * First: bet number of dofs for each cpu*/ + * First: get number of dofs for each cpu*/ alldofcount=(int*)xmalloc(num_procs*sizeof(int)); + #ifdef _HAVE_MPI_ MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else + alldofcount[0]=dofcount; + #endif /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ @@ -119,5 +123,10 @@ } } - MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + + #ifdef _HAVE_MPI_ + MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;iNumberOfNodes(analysis_type); @@ -162,5 +170,9 @@ * dealt with by another cpu. We take the minimum because we are going to manage dof assignment in increasing * order of cpu rank. This is also why we initialized this array to num_procs.*/ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)ranks,(void*)minranks,numnodes,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + for(i=0;iAddOption(option); - option=NULL; - } - - /*echo the dataset */ - //if (this->Size()) for(i=0;iSize();i++) ((Option*)this->GetObjectByOffset(i))->Echo(); -} -/*}}}*/ -#endif /*FUNCTION Options::~Options(){{{1*/ Options::~Options(){ Index: /issm/branches/trunk-jpl-damage/src/c/Container/Options.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Options.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Options.h (revision 12168) @@ -15,7 +15,4 @@ /*constructors, destructors*/ Options(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - Options(int istart, int nrhs, const mxArray* prhs[]); - #endif ~Options(); Index: /issm/branches/trunk-jpl-damage/src/c/Container/Results.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Results.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Results.cpp (revision 12168) @@ -65,88 +65,4 @@ /*}}}*/ /*FUNCTION Results::Write{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Results::Write(mxArray** pdataref){ - - int i,j; - int count; - - /*output: */ - mxArray* dataref=NULL; - mxArray* processeddataref=NULL; - mwSize nfields; - mwSize maxfields; - mwSize nsteps; - mwSize step; - const char **fnames = NULL; - int *enums = NULL; - int baseenum; - mwSize onebyone[2] = {1,1}; - mwSize ndim = 2; - - /*How many time steps do we have? : */ - nsteps=0; - for(i=0;iSize();i++){ - ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); - step=result->GetStep(); - if(step>nsteps)nsteps=step; - } - onebyone[0]=nsteps; - - /*How many field names do we have. First, figure out how many result types we have: */ - maxfields=(mwSize)this->Size(); - enums=(int*)xmalloc(maxfields*sizeof(int)); - for(i=0;iGetObjectByOffset(i); - enums[i]=result->InstanceEnum(); - } - /*Now, make result types unique: */ - for(i=0;i=0){//if <0, it means this enum was found to replicate another one previously - baseenum=enums[i]; - /*is the baseenum repeated later on?:*/ - for(j=i+1;j0)nfields++; - - /*Add 2 fields for time and step: */ - nfields=nfields+2; - - /*Fill the names of the structure field: */ - fnames=(const char**)xmalloc(nfields*sizeof(char*)); - count=0; - for(i=0;i0){ - fnames[count]=EnumToStringx(enums[i]); - count++; - } - } - /*don't forget the extra fields "time" and "step":*/ - fnames[nfields-2]="time"; - fnames[nfields-1]="step"; - - /*Initialize structure: */ - dataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); - - /*Fill each field: */ - for(i=0;iSize();i++){ //do not include the last one used for time - ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); - result->SetMatlabField(dataref); - } - - /*Now, process the patch in the dataref structure, by calling MatlabProcessPatch.m - *on the current dataref structure: */ - mexCallMATLAB(1,&processeddataref,1,&dataref, "MatlabProcessPatch"); - - /*Assign output pointers:*/ - *pdataref=processeddataref; -} -#else void Results::Write(Parameters* parameters){ @@ -167,4 +83,3 @@ } -#endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/Container/Results.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Results.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Results.h (revision 12168) @@ -26,9 +26,5 @@ /*numerics: {{{1*/ Results* SpawnTriaResults(int* indices); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void Write(mxArray** pdataref); - #else void Write(Parameters* parameters); - #endif /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.cpp (revision 12168) @@ -61,6 +61,10 @@ * First: bet number of dofs for each cpu*/ alldofcount=(int*)xmalloc(num_procs*sizeof(int)); + #ifdef _HAVE_MPI_ MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else + alldofcount[0]=dofcount; + #endif /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ @@ -85,5 +89,9 @@ vertex->ShowTrueDofs(truedofs); } + #ifdef _HAVE_MPI_ MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;i $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat < $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp /* * \file EnumToStringx.cpp: @@ -35,7 +35,7 @@ END #core -cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp #Footer -cat <> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat <> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp default : return "unknown"; @@ -57,5 +57,5 @@ #Build StringToEnumx.cpp {{{1 #Header -cat < $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp +cat < $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp /* * \file StringToEnumx.cpp: @@ -81,9 +81,9 @@ i2=120; for (( i=1 ; i<=100 ; i++ )); do - echo " if(stage==$i){" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " if(stage==$i){" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp awk -v i1=$i1 -v i2=$i2 '{if(NR>=i1 && NR<=i2) print $0 }' temp | - awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp - echo " else stage=$(($i+1));" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp - echo " }" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp + awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " else stage=$(($i+1));" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " }" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp if [ $i2 -ge $NUMENUMS ]; then break; fi @@ -93,5 +93,5 @@ #footer -cat <> $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp +cat <> $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp /*If we reach this point, the string provided has not been found*/ _error_("Enum %s not found",name); @@ -127,5 +127,5 @@ #}}} #Add case to matlabenum file{{{ - cat < $ISSM_TIER"/src/m/enum/"$(echo $NAMEENUM".m") + cat < $ISSM_DIR"/src/m/enum/"$(echo $NAMEENUM".m") function macro=$(echo $NAMEENUM)() %$(echo $NAMEENUM | awk {'print toupper($1)'}) - Enum of $(echo $NAME) Index: /issm/branches/trunk-jpl-damage/src/c/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 12168) @@ -4,17 +4,10 @@ #Library declaration {{{1 -#Compile serial library, and then try and compile parallel library -if NOSERIAL -if NOPARALLEL -lib_LIBRARIES = -else -lib_LIBRARIES = libpISSM.a libOverload.a -endif -else -if NOPARALLEL -lib_LIBRARIES = libISSM.a libOverload.a -else -lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a -endif +lib_LIBRARIES = libISSMCore.a libISSMModules.a libISSMOverload.a +if PYTHON +lib_LIBRARIES += libISSMPython.a +endif +if MATLAB +lib_LIBRARIES += libISSMMatlab.a endif #}}} @@ -22,5 +15,7 @@ #sources #Core sources{{{1 -core_sources = ./include/macros.h\ +core_sources = ./issm.h\ + ./issm-binding.h\ + ./include/macros.h\ ./include/typedefs.h\ ./include/types.h\ @@ -211,10 +206,4 @@ ./shared/Wrapper/ModuleBoot.cpp\ ./shared/Wrapper/ModuleEnd.cpp\ - ./toolkits/mpi/mpiincludes.h\ - ./toolkits/mpi/patches/mpipatches.h\ - ./toolkits/mpi/patches/DetermineLocalSize.cpp\ - ./toolkits/mpi/patches/MPI_Upperrow.cpp\ - ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ - ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ ./toolkits/metis/metisincludes.h\ ./toolkits/issm/issmtoolkit.h\ @@ -223,6 +212,4 @@ ./toolkits/issm/SeqMat.h\ ./toolkits/issm/SeqMat.cpp\ - ./toolkits/metis/patches/metispatches.h\ - ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ ./toolkits/triangle/triangleincludes.h\ ./toolkitsenums.h\ @@ -362,14 +349,14 @@ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h -dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ + ./modules/Dakotax/SpawnCoreParallel.cpp #}}} #Transient sources {{{1 -transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp -transient_psources = ./solutions/transient_core.cpp +transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp \ + ./solutions/transient_core.cpp #}}} #Steadystate sources {{{1 -steadystate_psources = ./solutions/steadystate_core.cpp\ - ./solutions/steadystateconvergence.cpp +steadystate_sources = ./solutions/steadystate_core.cpp\ + ./solutions/steadystateconvergence.cpp #}}} #Prognostic sources {{{1 @@ -377,6 +364,6 @@ ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp -prognostic_psources = ./solutions/prognostic_core.cpp + ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp\ + ./solutions/prognostic_core.cpp #}}} #Thermal sources {{{1 @@ -395,9 +382,8 @@ ./modules/ConstraintsStatex/ThermalConstraintsState.cpp\ ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ - ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp - -thermal_psources = ./solutions/thermal_core.cpp\ - ./solutions/enthalpy_core.cpp\ - ./solvers/solver_thermal_nonlinear.cpp + ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp \ + ./solutions/thermal_core.cpp\ + ./solutions/enthalpy_core.cpp\ + ./solvers/solver_thermal_nonlinear.cpp #}}} #Control sources {{{1 @@ -443,8 +429,6 @@ ./objects/Inputs/ControlInput.cpp\ ./shared/Numerics/BrentSearch.cpp\ - ./shared/Numerics/OptimalSearch.cpp\ - ./shared/Numerics/OptFunc.cpp - -control_psources=./solutions/control_core.cpp\ + ./shared/Numerics/OptimalSearch.cpp \ + ./solutions/control_core.cpp\ ./solutions/controltao_core.cpp\ ./solutions/controlrestart.cpp\ @@ -462,8 +446,7 @@ ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp - -hydrology_psources = ./solutions/hydrology_core.cpp\ - ./solutions/hydrology_core_step.cpp + ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp \ + ./solutions/hydrology_core.cpp\ + ./solutions/hydrology_core_step.cpp #}}} #Diagnostic sources {{{1 @@ -480,11 +463,11 @@ ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ - ./shared/Elements/CoordinateSystemTransform.cpp\ - ./shared/Elements/TransformLoadVectorCoord.cpp \ - ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformSolutionCoord.cpp -diagnostic_psources =./solutions/diagnostic_core.cpp\ - ./solvers/solver_stokescoupling_nonlinear.cpp + ./shared/Elements/CoordinateSystemTransform.cpp\ + ./shared/Elements/TransformLoadVectorCoord.cpp \ + ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformSolutionCoord.cpp\ + ./solutions/diagnostic_core.cpp\ + ./solvers/solver_stokescoupling_nonlinear.cpp #}}} #Balanced sources {{{1 @@ -492,6 +475,6 @@ ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp -balanced_psources = ./solutions/balancethickness_core.cpp + ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ + ./solutions/balancethickness_core.cpp #}}} #Responses sources {{{1 @@ -533,6 +516,6 @@ ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp -slope_psources = ./solutions/surfaceslope_core.cpp\ + ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\ + ./solutions/surfaceslope_core.cpp\ ./solutions/bedslope_core.cpp #}}} @@ -694,23 +677,4 @@ ./objects/KML/KMLFileReadUtils.h #}}} -#Matlab sources {{{1 -matlab_sources= ./toolkits/matlab/matlabincludes.h\ - ./toolkits/matlab/MatlabNArrayToNArray.cpp\ - ./toolkits/double/MatlabVectorToDoubleVector.cpp\ - ./toolkits/double/double.h\ - ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ - ./io/Matlab/matlabio.h\ - ./io/Matlab/CheckNumMatlabArguments.cpp\ - ./io/Matlab/mxGetAssignedField.cpp\ - ./io/Matlab/WriteMatlabData.cpp\ - ./io/Matlab/FetchMatlabData.cpp\ - ./io/Matlab/OptionParse.cpp -#}}} -#Python sources {{{1 -python_sources= ./io/Python/pythonio.h\ - ./io/Python/WritePythonData.cpp\ - ./io/Python/CheckNumPythonArguments.cpp\ - ./io/Python/FetchPythonData.cpp -#}}} #Petsc sources {{{1 petsc_sources= ./toolkits/petsc\ @@ -718,8 +682,4 @@ ./toolkits/petsc/patches/SolverEnum.h\ ./toolkits/petsc/patches/petscpatches.h\ - ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ - ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ - ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ ./toolkits/petsc/patches/VecTranspose.cpp\ ./toolkits/petsc/patches/VecToMPISerial.cpp\ @@ -732,4 +692,6 @@ ./toolkits/petsc/patches/SerialToVec.cpp\ ./toolkits/petsc/patches/VecFree.cpp\ + ./toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp\ + ./toolkits/petsc/patches/PetscVectorToDoubleVector.cpp\ ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ ./toolkits/petsc/patches/KSPFree.cpp\ @@ -754,6 +716,48 @@ #}}} -#Serialsources {{{1 -serial_sources= ./objects/Options/Option.cpp\ +#Mpi sources {{{1 +mpi_sources= ./toolkits/mpi/mpiincludes.h\ + ./toolkits/mpi/patches/mpipatches.h\ + ./toolkits/mpi/patches/DetermineLocalSize.cpp\ + ./toolkits/mpi/patches/MPI_Upperrow.cpp\ + ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ + ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp +#}}} +#Metis sources {{{1 +metis_sources= ./toolkits/metis/patches/metispatches.h\ + ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp +#}}} +#Python sources {{{1 +python_sources= ./python/io/pythonio.h\ + ./python/python-binding.h\ + ./python/io/WritePythonData.cpp\ + ./python/io/CheckNumPythonArguments.cpp\ + ./python/io/FetchPythonData.cpp + +#}}} +#Matlab sources {{{1 +matlab_sources= ./toolkits/matlab/matlabincludes.h\ + ./matlab/matlab-binding.h\ + ./matlab/io/matlabio.h\ + ./matlab/io/MatlabNArrayToNArray.cpp\ + ./matlab/io/CheckNumMatlabArguments.cpp\ + ./matlab/io/mxGetAssignedField.cpp\ + ./matlab/io/WriteMatlabData.cpp\ + ./matlab/io/FetchMatlabData.cpp\ + ./matlab/io/OptionParse.cpp\ + ./matlab/io/MatlabMatrixToMatrix.cpp\ + ./matlab/io/MatlabVectorToVector.cpp\ + ./matlab/io/MatlabVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ + ./matlab/io/MatlabMatrixToSeqMat.cpp\ + ./matlab/io/MatlabVectorToSeqVec.cpp +#}}} +#Matlab and Petsc sources {{{1 +matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ + ./matlab/io/MatlabVectorToPetscVector.cpp + +#}}} +#Modules sources{{{1 +module_sources= ./objects/Options/Option.cpp\ ./objects/Options/Option.h\ ./objects/Options/OptionDouble.cpp\ @@ -769,4 +773,6 @@ ./objects/Options/OptionUtilities.cpp\ ./objects/Options/OptionUtilities.h\ + ./shared/Alloc/alloc_module.h\ + ./shared/Alloc/alloc_module.cpp\ ./shared/Threads/issm_threads.h\ ./shared/Threads/LaunchThread.cpp\ @@ -790,5 +796,4 @@ ./modules/Chacox/chaco_seconds.cpp\ ./modules/Chacox/user_params.cpp\ - ./modules/Dakotax/SpawnCoreSerial.cpp\ ./modules/TriaSearchx/TriaSearchx.h\ ./modules/TriaSearchx/TriaSearchx.cpp\ @@ -815,4 +820,6 @@ ./modules/HoleFillerx/HoleFillerx.cpp\ ./modules/HoleFillerx/HoleFillerx.h\ + ./modules/Krigingx/Krigingx.cpp\ + ./modules/Krigingx/Krigingx.h\ ./modules/AverageFilterx/AverageFilterx.cpp\ ./modules/AverageFilterx/AverageFilterx.h\ @@ -841,67 +848,55 @@ #}}} +#{{{1 Conditional build-up of sources #ISSM sources are a combination of core sources and sources related to specific capabilities (which can #be activated by autotools conditionals -#{{{1 + #First the core issm_sources = $(core_sources) -issm_psources = #Now the optional source if DAKOTA issm_sources += $(dakota_sources) -issm_psources += $(dakota_psources) endif if PETSC issm_sources += $(petsc_sources) -issm_psources += $(petsc_psources) endif if GSL issm_sources += $(gsl_sources) -issm_psources += $(gsl_psources) -endif - +endif if TRANSIENT issm_sources += $(transient_sources) -issm_psources += $(transient_psources) endif if STEADYSTATE issm_sources += $(steadystate_sources) -issm_psources += $(steadystate_psources) endif if PROGNOSTIC issm_sources += $(prognostic_sources) -issm_psources += $(prognostic_psources) endif if THERMAL issm_sources += $(thermal_sources) -issm_psources += $(thermal_psources) endif if CONTROL issm_sources += $(control_sources) -issm_psources += $(control_psources) endif if HYDROLOGY issm_sources += $(hydrology_sources) -issm_psources += $(hydrology_psources) endif if DIAGNOSTIC issm_sources += $(diagnostic_sources) -issm_psources += $(diagnostic_psources) endif if BALANCED issm_sources += $(balanced_sources) -issm_psources += $(balanced_psources) endif @@ -912,5 +907,4 @@ if SLOPE issm_sources += $(slope_sources) -issm_psources += $(slope_psources) endif @@ -926,47 +920,54 @@ issm_sources += $(threed_sources) endif -#}}} - -#ISSM serial library {{{1 -if SERIAL -libISSM_a_SOURCES = $(issm_sources) -libISSM_a_SOURCES += $(serial_sources) -libISSM_a_SOURCES += $(bamg_sources) -libISSM_a_SOURCES += $(kml_sources) -libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) -#libISSM_a_CXXFLAGS = -D_SERIAL_ -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER $(CXXFLAGS) $(CXXOPTFLAGS) + +if MPI +issm_sources += $(mpi_sources) +endif + +if METIS +issm_sources += $(metis_sources) +endif + +if PETSC +if MATLAB +issm_sources += $(matlabpetsc_sources) +endif +endif + + +#}}} +#Library flags and sources {{{1 +ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) + +libISSMCore_a_SOURCES = $(issm_sources) +libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS) + +if MODULES +libISSMModules_a_SOURCES = $(module_sources) +libISSMModules_a_SOURCES += $(bamg_sources) +libISSMModules_a_SOURCES += $(kml_sources) +libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) if PYTHON -libISSM_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API -libISSM_a_SOURCES += $(python_sources) +libISSMPython_a_SOURCES = $(python_sources) +libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS) endif if MATLAB -libISSM_a_SOURCES += $(matlab_sources) -endif - -endif -#}}} -#ISSM parallel library {{{1 -if PARALLEL -libpISSM_a_SOURCES = $(issm_sources) -libpISSM_a_SOURCES += $(issm_psources) -libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) +libISSMMatlab_a_SOURCES = $(matlab_sources) +libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS) +endif endif #}}} #Overload library, to overload any non-standard symbols. {{{1 -libOverload_a_SOURCES = ./shared/String/stricmp.c -libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) +libISSMOverload_a_SOURCES = ./shared/String/stricmp.c +libISSMOverload_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) $(CFLAGS) #}}} #Executable {{{1 -if NOPARALLEL -bin_PROGRAMS = -else bin_PROGRAMS = issm -endif #Standard libraries -LDADD = ./libpISSM.a ./libOverload.a +LDADD = ./libISSMCore.a ./libISSMOverload.a #External packages @@ -974,22 +975,21 @@ issm_SOURCES = solutions/issm.cpp -issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) +issm_CXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) #}}} #Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ if ADIC2 -lib_LIBRARIES += libAD.a libpISSMRose.a +lib_LIBRARIES += libAD.a libISSMRose.a #ADIC2 library, for automatic differentiation #libAD_a_SOURCES = ./mini1.ad.c libAD_a_SOURCES = -libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) - +libAD_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) #test rose preprocessing %.r2cpp.cpp : %.cpp - testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< -libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) -libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) + testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_C_ -I. -I../.. $(INCLUDES) $< +libISSMRose_a_SOURCES = $(libISSMCore_a_SOURCES:.cpp=.r2cpp.cpp) +libISSMRose_a_CXXFLAGS= -fPIC -D_C_ $(CXXOPTFLAGS) @@ -1003,7 +1003,7 @@ #Executable bin_PROGRAMS += issmRose.exe -issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) +issmRose_exe_LDADD = ./libISSMRose.a $(LDADD) issmRose_exe_SOURCES = solutions/issm.cpp -issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) +issmRose_exe_CXXFLAGS= -fPIC $(CXXOPTFLAGS) $(COPTFLAGS) LDADD += $(ADIC2LIB) Index: /issm/branches/trunk-jpl-damage/src/c/include/macros.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/include/macros.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/include/macros.h (revision 12168) @@ -40,39 +40,14 @@ #endif /*}}}*/ - -/* MODULEBOOT/MODULEEND {{{1*/ +/* ISSMBOOT/ISSMEND {{{1*/ /*The following macros hide the error exception handling in a matlab module. Just put - * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * ISSMBOOT(); and ISSMEND(); at the beginning and end of a module, and c++ exceptions * will be trapped. Really nifty!*/ -#ifdef _SERIAL_ -#ifdef _HAVE_MATLAB_ //{{{2 -#define MODULEBOOT(); ModuleBoot(); \ +#define ISSMBOOT(); \ try{ -#define MODULEEND(); ModuleEnd(); }\ - catch(ErrorException &exception){\ - exception.Report(); \ - mexErrMsgTxt(""); \ - }\ - catch (exception& e) {\ - _printf_(true,"Standard exception: %s\n",e.what());\ - mexErrMsgTxt(" ");\ - } -#endif //}}} -#ifdef _HAVE_PYTHON_ //{{{2 -#define MODULEBOOT(); ModuleBoot(); \ - PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; - -#define MODULEEND(); ModuleEnd(); \ - return output; -#endif //}}} -#else -//{{{2 -#define MODULEBOOT(); \ - try{ - -#define MODULEEND(); }\ +#define ISSMEND(); }\ catch(ErrorException &exception){\ exception.Report(); \ @@ -82,50 +57,9 @@ _printf_(true,"Standard exception: %s\n",e.what());\ return 1;\ + }\ + catch(...){\ + _printf_(true,"An unexpected error occurred");\ } -//}}} -#endif /*}}}*/ -/* WRAPPER {{{1*/ -#ifdef _HAVE_MATLAB_ -#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) -#endif -#ifdef _HAVE_PYTHON_ -#define WRAPPER(modulename,...) \ -\ -static PyObject* modulename(PyObject* self,PyObject* args);\ -static PyMethodDef modulename##_funcs[] = {\ - {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ - {NULL,NULL,0,NULL}\ -};\ -\ -static struct PyModuleDef modulename##module= {\ - PyModuleDef_HEAD_INIT,\ - #modulename, /* name of module */\ - NULL, /* module documentation, may be NULL */\ - -1, /* size of per-interpreter state of the module,\ - or -1 if the module keeps state in global variables. */\ - modulename##_funcs\ -};\ -\ -PyMODINIT_FUNC PyInit_##modulename(void){\ -\ - import_array();\ - return PyModule_Create(&modulename##module);\ -}\ -\ -static PyObject* modulename(PyObject* self,PyObject* args) #endif - -/*}}}*/ -/* CHECKARGUMENTS {{{1*/ -#ifdef _HAVE_MATLAB_ -#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) -#endif -#ifdef _HAVE_PYTHON_ -#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) -#endif -/*}}}*/ - - -#endif Index: /issm/branches/trunk-jpl-damage/src/c/include/types.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/include/types.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/include/types.h (revision 12168) @@ -16,12 +16,4 @@ /*Define abstract type for I/O: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -typedef const mxArray* ConstDataHandle; //serially, we are reading data from a matlab array. -typedef mxArray* DataHandle; -#else -typedef FILE* ConstDataHandle; //in parallel, we are reading data from a file. -typedef FILE* DataHandle; -#endif enum param_type { STRING, INTEGER, STRINGARRAY, DOUBLE, DOUBLEVEC, DOUBLEMAT, PETSCVEC, PETSCMAT }; Index: /issm/branches/trunk-jpl-damage/src/c/io/PrintfFunction.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/PrintfFunction.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/io/PrintfFunction.cpp (revision 12168) @@ -8,8 +8,4 @@ #include "../shared/shared.h" #include "../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif int PrintfFunction(const char* format,...){ @@ -53,9 +49,5 @@ /*Ok, if we are running in parallel, get node 0 to print*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mexPrintf(buffer); -#else if(my_rank==0)printf(buffer); -#endif /*Clean up and return*/ Index: /issm/branches/trunk-jpl-damage/src/c/io/io.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/io.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/io/io.h (revision 12168) @@ -15,12 +15,4 @@ #include "./Disk/diskio.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "./Matlab/matlabio.h" -#endif - -#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) -#include "./Python/pythonio.h" -#endif - /*printf: */ int PrintfFunction(const char* format,...); Index: /issm/branches/trunk-jpl-damage/src/c/issm-binding.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/issm-binding.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/issm-binding.h (revision 12168) @@ -0,0 +1,18 @@ +#ifndef _ISSM_BINDING_H_ +#define _ISSM_BINDING_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _HAVE_MATLAB_MODULES_ +#include "./matlab/matlab-binding.h" +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +#include "./python/python-binding.h" +#endif + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/matlab/include/matlab_macros.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/include/matlab_macros.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/include/matlab_macros.h (revision 12168) @@ -0,0 +1,47 @@ +/* \file matlab macros.h + * \brief: macros used for the matlab bindings + */ + +/*Header {{{1*/ +#ifndef _MATLAB_MACROS_H_ +#define _MATLAB_MACROS_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +/*}}}*/ + +#ifdef _HAVE_MATLAB_ +/* MODULEBOOT/MODULEEND {{{1*/ + +/*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ +//exception.Report(); + +#define MODULEBOOT(); ModuleBoot(); \ + try{ + +#define MODULEEND(); ModuleEnd(); }\ + catch(ErrorException &exception){\ + mexErrMsgTxt("ISSM Error"); \ + }\ + catch (exception &e){\ + mexErrMsgTxt(exprintf("Standard exception: %s\n",e.what()));\ + }\ + catch(...){\ + mexErrMsgTxt("An unexpected error occurred");\ + } +//}}} +/* WRAPPER {{{1*/ +#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) + +/*}}}*/ +/* CHECKARGUMENTS {{{1*/ +#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) +/*}}}*/ +#endif + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/CheckNumMatlabArguments.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12168) @@ -0,0 +1,31 @@ +/*!\file CheckNumMatlabArguments.cpp: + * \brief: check number of arguments and report an usage error message. + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "../../shared/Exceptions/exceptions.h" +#include "../../include/include.h" +#include "mex.h" + +int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* __FUNCT__, void (*function)( void )){ + + /*checks on arguments on the matlab side: */ + if (nrhs==0 && nlhs==0) { + /*unless NLHS=0 and NRHS=0, we are just asking for documentation: */ + if (NRHS==0 && NLHS==0)return 1; + /* special case: */ + function(); + _error_("usage: see above"); + } + else if (nlhs!=NLHS || nrhs!=NRHS ) { + function(); + _error_("usage error."); + } + return 1; +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp (revision 12168) @@ -0,0 +1,638 @@ +/*\file FetchData.cpp: + * \brief: general I/O interface to fetch data in matlab + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "./matlabio.h" + +/*Primitive data types*/ +/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ +void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){ + + double* outmatrix=NULL; + int outmatrix_rows,outmatrix_cols; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else if(mxIsClass(dataref,"double") || mxIsClass(dataref,"single")){ + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else{ + /*Convert matlab matrix to double* matrix: */ + MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref); + } + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pmatrix=outmatrix; + if (pM)*pM=outmatrix_rows; + if (pN)*pN=outmatrix_cols; + +} +/*}}}*/ +/*FUNCTION FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{1*/ +void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){ + + double* outmatrix=NULL; + int outmatrix_numel,outmatrix_ndims; + int* outmatrix_size=NULL; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_numel=0; + outmatrix_ndims=0; + outmatrix_size =NULL; + outmatrix=NULL; + } + else if (mxIsClass(dataref,"double") ){ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){ + outmatrix_numel=0; + outmatrix_ndims=0; + outmatrix_size =NULL; + outmatrix=NULL; + } + else{ + + /*Convert matlab n-dim array to double* matrix: */ + MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); + } + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pmatrix=outmatrix; + if (pnumel)*pnumel=outmatrix_numel; + if (pndims)*pndims=outmatrix_ndims; + if (psize )*psize =outmatrix_size; + else xfree((void**)&outmatrix_size); + +} +/*}}}*/ +/*FUNCTION FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ +void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){ + + int i,outmatrix_rows,outmatrix_cols; + double *doublematrix=NULL; + int *outmatrix=NULL; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else if (mxIsClass(dataref,"double") ){ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else{ + + /*Convert matlab matrix to double* matrix: */ + MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref); + + /*Convert double matrix into integer matrix: */ + outmatrix=(int*)xmalloc(outmatrix_rows*outmatrix_cols*sizeof(int)); + for(i=0;iVertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); + FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); + FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], mxGetAssignedField(dataref,0,"Corners")); + FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],mxGetAssignedField(dataref,0,"RequiredVertices")); + FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], mxGetAssignedField(dataref,0,"RequiredEdges")); + FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); + FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],mxGetAssignedField(dataref,0,"SubDomains")); + + /*Assign output pointers:*/ + *pbamggeom=bamggeom; +} +/*}}}*/ +/*FUNCTION FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){{{1*/ +void FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){ + + /*Initialize output*/ + BamgMesh* bamgmesh=new BamgMesh(); + + /*Fetch all fields*/ + FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); + FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); + FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], mxGetAssignedField(dataref,0,"Triangles")); + FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); + FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomEdge")); + FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomVertex")); + FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], mxGetAssignedField(dataref,0,"EdgesOnGeomEdge")); + FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],mxGetAssignedField(dataref,0,"IssmSegments")); + + /*Assign output pointers:*/ + *pbamgmesh=bamgmesh; +} +/*}}}*/ +/*FUNCTION FetchData(BamgOpts** pbamgopts,const mxArray* dataref){{{1*/ +void FetchData(BamgOpts** pbamgopts,const mxArray* dataref){ + + /*Initialize output*/ + BamgOpts* bamgopts=new BamgOpts(); + + /*Fetch all fields*/ + FetchData(&bamgopts->anisomax,mxGetField(dataref,0,"anisomax")); + FetchData(&bamgopts->cutoff,mxGetField(dataref,0,"cutoff")); + FetchData(&bamgopts->coeff,mxGetField(dataref,0,"coeff")); + FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg")); + FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation")); + FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype")); + FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle")); + FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv")); + FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv")); + FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype")); + FetchData(&bamgopts->nbjacobi,mxGetField(dataref,0,"nbjacobi")); + FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth")); + FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega")); + FetchData(&bamgopts->power,mxGetField(dataref,0,"power")); + FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose")); + + FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack")); + FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric")); + FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices")); + FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners")); + + FetchData(&bamgopts->hmin,mxGetField(dataref,0,"hmin")); + FetchData(&bamgopts->hmax,mxGetField(dataref,0,"hmax")); + FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],mxGetField(dataref,0,"hminVertices")); + FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],mxGetField(dataref,0,"hmaxVertices")); + FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],mxGetField(dataref,0,"hVertices")); + FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],mxGetField(dataref,0,"metric")); + FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],mxGetField(dataref,0,"field")); + FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],mxGetField(dataref,0,"err")); + + /*Additional checks*/ + bamgopts->Check(); + + /*Assign output pointers:*/ + *pbamgopts=bamgopts; +} +/*}}}*/ +/*FUNCTION FetchData(Options** poptions,const mxArray* dataref){{{1*/ +void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref){ + + char *name = NULL; + Option *option = NULL; + + /*Initialize output*/ + Options* options=new Options(); + + /*Fetch all options*/ + for (int i=istart; iAddOption(option); + option=NULL; + } + + /*Assign output pointers:*/ + *poptions=options; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 12168) @@ -0,0 +1,101 @@ +/* \file MatlabMatrixToDoubleMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a double* pointer + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + + int i,j,count,rows,cols; + double *pmxdoublematrix = NULL; + float *pmxsinglematrix = NULL; + + /*output: */ + double* matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ + pmxdoublematrix=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); + + if(rows*cols){ + matrix=(double*)xcalloc(rows*cols,sizeof(double)); + + /*Now, get ir,jc and pr: */ + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + + /*Now, start inserting data into double* matrix: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "./matlabio.h" +#include "../../objects/objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" + +/*}}}*/ + +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ + + int dummy; + Matrix* matrix=NULL; + + /*allocate matrix object: */ + matrix=new Matrix(); + + #ifdef _HAVE_PETSC_ + MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); + #else + matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); + #endif + + return matrix; +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12168) @@ -0,0 +1,120 @@ +/* \file MatlabMatrixToPetscMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix: + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + + int rows, cols; + double* mxmatrix_ptr=NULL; + double* tmatrix=NULL; + int ierr; + int i,j; + + /*output: */ + Mat matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*petsc indices: */ + int* idxm=NULL; + int* idxn=NULL; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ + mxmatrix_ptr=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); + nnz=mxGetNzmax(mxmatrix); + if(rows){ + nz=(int)((double)nnz/(double)rows); + } + else{ + nz=0; + } + + ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxmatrix); + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + + /*Now, start inserting data into sparse matrix: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "../../toolkits/toolkits.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +/*}}}*/ + +SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ + + SeqMat* output=NULL; + + output=new SeqMat(); + MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); + return output; + +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabNArrayToNArray.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12168) @@ -0,0 +1,272 @@ +/* \file MatlabNArrayToNArray.cpp + * \brief: convert a sparse or dense matlab n-dimensional array to cpp n-dimensional array + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../shared/shared.h" +#include "../../include/include.h" + +#include + +/*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{1*/ +int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){ + + int i,j,rows,cols; + int numel,ndims; + int *size,*dims; + double* mxmatrix_ptr=NULL; + const mwSize* ipt=NULL; + + /*output: */ + double* matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*get Matlab matrix information: */ + numel=mxGetNumberOfElements(mxmatrix); + ndims=mxGetNumberOfDimensions(mxmatrix); + ipt =mxGetDimensions(mxmatrix); + size =(int *) xcalloc(ndims,sizeof(int)); + for (i=0; i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ + + int rows,cols; + double* mxvector_ptr=NULL; + int ierr; + int i,j; + + /*output: */ + double* vector=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*Ok, first check if we are dealing with a sparse or full vector: */ + if (mxIsSparse(mxvector)){ + + /*Dealing with sparse vector: recover size first: */ + mxvector_ptr=(double*)mxGetPr(mxvector); + rows=mxGetM(mxvector); + cols=mxGetN(mxvector); + nnz=mxGetNzmax(mxvector); + + /*Check that input is actualy a vector*/ + if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); + + nz=(int)((double)nnz/(double)rows); + + if(rows){ + vector=(double*)xcalloc(rows,sizeof(double)); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxvector); + ir=mxGetIr(mxvector); + jc=mxGetJc(mxvector); + + /*Now, start inserting data into sparse vector: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ + + int rows, cols; + double* mxvector_ptr=NULL; + int ierr; + int i,j; + + /*output: */ + Vec vector=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*petsc indices: */ + int* idxm=NULL; + + /*Ok, first check if we are dealing with a sparse or full vector: */ + if (mxIsSparse(mxvector)){ + + /*Dealing with sparse vector: recover size first: */ + mxvector_ptr=(double*)mxGetPr(mxvector); + rows=mxGetM(mxvector); + cols=mxGetN(mxvector); + nnz=mxGetNzmax(mxvector); + nz=(int)((double)nnz/(double)rows); + + ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxvector); + ir=mxGetIr(mxvector); + jc=mxGetJc(mxvector); + + /*Now, start inserting data into sparse vector: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "../../toolkits/toolkits.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +/*}}}*/ + +SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ + + SeqVec* output=NULL; + + output=new SeqVec(); + MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); + return output; + +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabVectorToVector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12168) @@ -0,0 +1,39 @@ +/*!\file MatlabVectorToVector.cpp + */ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "./matlabio.h" +#include "../../objects/objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" + +/*}}}*/ + +Vector* MatlabVectorToVector(const mxArray* mxvector){ + + int dummy; + Vector* vector=NULL; + + /*allocate vector object: */ + vector=new Vector(); + + #ifdef _HAVE_PETSC_ + MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); + #else + vector->vector=MatlabVectorToSeqVec(mxvector); + #endif + + return vector; +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp (revision 12168) @@ -0,0 +1,191 @@ +/*\file OptionParse.c + *\brief: functions to parse the mex options. + */ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../shared/shared.h" +#include "../../io/io.h" +#include "../../include/include.h" +#include "./matlabio.h" + +#include + +/*FUNCTION OptionDoubleParse {{{1*/ +OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]){ + + OptionDouble *odouble = NULL; + + /*check and parse the name */ + odouble=new OptionDouble; + odouble->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"double")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",odouble->name,"double",odouble->name,mxGetClassName(prhs[0])); + } + + FetchData(&odouble->values,&odouble->numel,&odouble->ndims,&odouble->size,prhs[0]); + + return(odouble); +}/*}}}*/ +/*FUNCTION OptionLogicalParse {{{1*/ +OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]){ + + OptionLogical *ological = NULL; + + /*check and parse the name */ + ological=new OptionLogical; + ological->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ological->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"logical")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ological->name,"logical",ological->name,mxGetClassName(prhs[0])); + } + + FetchData(&ological->values,&ological->numel,&ological->ndims,&ological->size,prhs[0]); + + return(ological); +}/*}}}*/ +/*FUNCTION OptionCharParse {{{1*/ +OptionChar* OptionCharParse( char* name, const mxArray* prhs[]){ + + OptionChar *ochar = NULL; + + /*check and parse the name */ + ochar=new OptionChar; + ochar->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"char")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ochar->name,"char",ochar->name,mxGetClassName(prhs[0])); + } + + FetchData(&ochar->values,&ochar->numel,&ochar->ndims,&ochar->size,prhs[0]); + + return(ochar); +}/*}}}*/ +/*FUNCTION OptionStructParse {{{1*/ +OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]){ + + int i; + char namei[161]; + OptionStruct *ostruct = NULL; + Option *option = NULL; + const mwSize *ipt = NULL; + const mxArray *structi; + mwIndex sindex; + + /*check and parse the name */ + ostruct=new OptionStruct; + ostruct->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"struct")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ostruct->name,"struct",ostruct->name,mxGetClassName(prhs[0])); + } + + ostruct->numel=mxGetNumberOfElements(prhs[0]); + ostruct->ndims=mxGetNumberOfDimensions(prhs[0]); + ipt =mxGetDimensions(prhs[0]); + ostruct->size =(int *) xmalloc(ostruct->ndims*sizeof(int)); + for (i=0; indims; i++) ostruct->size[i]=(int)ipt[i]; + if (ostruct->numel) ostruct->values=(Options**) xmalloc(ostruct->numel*sizeof(Options *)); + + /*loop through and process each element of the struct array */ + for (sindex=0; sindexnumel; sindex++) { + ostruct->values[sindex]=new Options; + + /*loop through and process each field for the element */ + for (i=0; ivalues[sindex]->AddObject((Object*)option); + option=NULL; + } + } + + return(ostruct); +}/*}}}*/ +/*FUNCTION OptionCellParse {{{1*/ +OptionCell* OptionCellParse( char* name, const mxArray* prhs[]){ + + int i; + int *dims; + char namei[161]; + char cstr[81]; + OptionCell *ocell = NULL; + Option *option = NULL; + const mwSize *ipt = NULL; + const mxArray *celli; + mwIndex cindex; + + /*check and parse the name */ + ocell=new OptionCell; + ocell->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"cell")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ocell->name,"cell",ocell->name,mxGetClassName(prhs[0])); + } + + ocell->numel=mxGetNumberOfElements(prhs[0]); + ocell->ndims=mxGetNumberOfDimensions(prhs[0]); + ipt =mxGetDimensions(prhs[0]); + ocell->size =(int *) xmalloc(ocell->ndims*sizeof(int)); + for (i=0; indims; i++) ocell->size[i]=(int)ipt[i]; + ocell->values=new Options; + + /*loop through and process each element of the cell array */ + dims=(int *) xmalloc(ocell->ndims*sizeof(int)); + for (cindex=0; cindexnumel; cindex++) { + ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims); + StringFromDims(cstr,dims,ocell->ndims); + #ifdef _INTEL_WIN_ + _snprintf(namei,161,"%s%s",name,cstr); + #else + snprintf(namei,161,"%s%s",name,cstr); + #endif + celli=mxGetCell(prhs[0],cindex); + + option=(Option*)OptionParse(namei,&celli); + ocell->values->AddObject((Object*)option); + option=NULL; + } + xfree((void**)&dims); + + return(ocell); +}/*}}}*/ +/*FUNCTION OptionParse{{{1*/ +Option* OptionParse(char* name, const mxArray* prhs[]){ + + Option *option = NULL; + mxArray *lhs[1]; + + /*parse the value according to the matlab data type */ + if (mxIsClass(prhs[0],"double")) option=(Option*)OptionDoubleParse(name,prhs); + else if(mxIsClass(prhs[0],"logical")) option=(Option*)OptionLogicalParse(name,prhs); + else if(mxIsClass(prhs[0],"char")) option=(Option*)OptionCharParse(name,prhs); + else if(mxIsClass(prhs[0],"struct")) option=(Option*)OptionStructParse(name,prhs); + else if(mxIsClass(prhs[0],"cell")) option=(Option*)OptionCellParse(name,prhs); + else { + _printf_(true," Converting value of option \"%s\" from unrecognized class \"%s\" to class \"%s\".\n",name,mxGetClassName(prhs[0]),"struct"); + if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) { + option=(Option*)OptionStructParse(name,(const mxArray**)lhs); + mxDestroyArray(lhs[0]); + } + else _error_("Second argument value of option \"%s\" is of unrecognized class \"%s\".",name,mxGetClassName(prhs[0])); + } + + return(option); +}/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/PrintfFunction.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/PrintfFunction.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/PrintfFunction.cpp (revision 12168) @@ -0,0 +1,58 @@ +/*\file PrintfFunction.c + *\brief: this function is used by the _printf_ macro, to take into account the + *fact we may be running on a cluster. + */ + +#include +#include +#include "../../shared/shared.h" +#include "../../include/include.h" + +#include "mex.h" + +int PrintfFunction(char* format,...){ + /*http://linux.die.net/man/3/vsnprintf*/ + + /*string to be printed: */ + char *buffer = NULL; + int n,size = 100; + int string_size; + extern int my_rank; + extern int num_procs; + + //variable list of arguments + va_list args; + + while(true){ + + /*allocate buffer for given string size*/ + buffer=(char*)xmalloc(size*sizeof(char)); + + /* Try to print in the allocated space. */ + va_start(args, format); +#ifndef WIN32 + n=vsnprintf(buffer,size,format,args); +#else + n=vsnprintf(buffer,size,format,args); +#endif + va_end(args); + + /* If that worked, return the string. */ + if(n>-1 && n-1) /* glibc 2.1 */ + size=n+1; /* precisely what is needed */ + else /* glibc 2.0 */ + size*=2; /* twice the old size */ + + xfree((void**)&buffer); + } + + /*Ok, if we are running in parallel, get node 0 to print*/ + if(my_rank==0)printf(buffer); + + /*Clean up and return*/ + xfree((void**)&buffer); + return 1; +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/WriteMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/WriteMatlabData.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/WriteMatlabData.cpp (revision 12168) @@ -0,0 +1,310 @@ +/* \file WriteData.c: + * \brief: general interface for writing data + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../include/include.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +#include + + +/*Primitive data types*/ +/*FUNCTION WriteData(mxArray** pdataref,double* matrix, int M,int N){{{1*/ +void WriteData(mxArray** pdataref,double* matrix, int M,int N){ + + mxArray *dataref = NULL; + double *tmatrix = NULL; + + if(matrix){ + /*create the matlab matrixwith Matlab's memory manager */ + tmatrix=(double*)mxMalloc(M*N*sizeof(double)); + for(int i=0;iVerticesSize[0], bamggeom->VerticesSize[1], bamggeom->Vertices); + i++; SetStructureField(dataref,"Edges", bamggeom->EdgesSize[0], bamggeom->EdgesSize[1], bamggeom->Edges); + i++; SetStructureField(dataref,"TangentAtEdges", bamggeom->TangentAtEdgesSize[0], bamggeom->TangentAtEdgesSize[1], bamggeom->TangentAtEdges); + i++; SetStructureField(dataref,"RequiredVertices",bamggeom->RequiredVerticesSize[0],bamggeom->RequiredVerticesSize[1],bamggeom->RequiredVertices); + i++; SetStructureField(dataref,"RequiredEdges", bamggeom->RequiredEdgesSize[0], bamggeom->RequiredEdgesSize[1], bamggeom->RequiredEdges); + i++; SetStructureField(dataref,"CrackedEdges", bamggeom->CrackedEdgesSize[0], bamggeom->CrackedEdgesSize[1], bamggeom->CrackedEdges); + i++; SetStructureField(dataref,"SubDomains", bamggeom->SubDomainsSize[0], bamggeom->SubDomainsSize[1], bamggeom->SubDomains); + _assert_(i==numfields); + + /*Assign output*/ + *pdataref=dataref; +} +/*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,BamgMesh* bamgmesh){{{1*/ +void WriteData(mxArray** pdataref,BamgMesh* bamgmesh){ + + /*Intermediary*/ + int i; + mxArray *dataref = NULL; + const int numfields = 16; + const char *fnames[numfields]; + mwSize ndim = 2; + mwSize dimensions[2] = {1,1}; + + /*Initialize field names*/ + i=0; + fnames[i++] = "Triangles"; + fnames[i++] = "Vertices"; + fnames[i++] = "Edges"; + fnames[i++] = "IssmSegments"; + fnames[i++] = "IssmEdges"; + fnames[i++] = "Quadrilaterals"; + fnames[i++] = "VerticesOnGeomVertex"; + fnames[i++] = "VerticesOnGeomEdge"; + fnames[i++] = "EdgesOnGeomEdge"; + fnames[i++] = "SubDomains"; + fnames[i++] = "SubDomainsFromGeom"; + fnames[i++] = "ElementConnectivity"; + fnames[i++] = "NodalConnectivity"; + fnames[i++] = "NodalElementConnectivity"; + fnames[i++] = "CrackedVertices"; + fnames[i++] = "CrackedEdges"; + _assert_(i==numfields); + + /*Initialize Matlab structure*/ + dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames); + + /*set each matlab each field*/ + i=0; + i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles); + i++; SetStructureField(dataref,"Vertices",bamgmesh->VerticesSize[0], bamgmesh->VerticesSize[1],bamgmesh->Vertices); + i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges); + i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments); + i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges); + i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals); + i++; SetStructureField(dataref,"VerticesOnGeomVertex",bamgmesh->VerticesOnGeomVertexSize[0],bamgmesh->VerticesOnGeomVertexSize[1], bamgmesh->VerticesOnGeomVertex); + i++; SetStructureField(dataref,"VerticesOnGeomEdge",bamgmesh->VerticesOnGeomEdgeSize[0],bamgmesh->VerticesOnGeomEdgeSize[1], bamgmesh->VerticesOnGeomEdge); + i++; SetStructureField(dataref,"EdgesOnGeomEdge", bamgmesh->EdgesOnGeomEdgeSize[0], bamgmesh->EdgesOnGeomEdgeSize[1],bamgmesh->EdgesOnGeomEdge); + i++; SetStructureField(dataref,"SubDomains",bamgmesh->SubDomainsSize[0], bamgmesh->SubDomainsSize[1],bamgmesh->SubDomains); + i++; SetStructureField(dataref,"SubDomainsFromGeom", bamgmesh->SubDomainsFromGeomSize[0], bamgmesh->SubDomainsFromGeomSize[1],bamgmesh->SubDomainsFromGeom); + i++; SetStructureField(dataref,"ElementConnectivity",bamgmesh->ElementConnectivitySize[0],bamgmesh->ElementConnectivitySize[1], bamgmesh->ElementConnectivity); + i++; SetStructureField(dataref,"NodalConnectivity",bamgmesh->NodalConnectivitySize[0],bamgmesh->NodalConnectivitySize[1], bamgmesh->NodalConnectivity); + i++; SetStructureField(dataref,"NodalElementConnectivity", bamgmesh->NodalElementConnectivitySize[0], bamgmesh->NodalElementConnectivitySize[1],bamgmesh->NodalElementConnectivity); + i++; SetStructureField(dataref,"CrackedVertices", bamgmesh->CrackedVerticesSize[0],bamgmesh->CrackedVerticesSize[1], bamgmesh->CrackedVertices); + i++; SetStructureField(dataref,"CrackedEdges",bamgmesh->CrackedEdgesSize[0], bamgmesh->CrackedEdgesSize[1],bamgmesh->CrackedEdges); + _assert_(i==numfields); + + /*Assign output*/ + *pdataref=dataref; +} +/*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ +void WriteData(mxArray** pdataref,Matrix* matrix){ + + int i,j; + int rows,cols; + mxArray *dataref = NULL; + double *matrix_ptr = NULL; + double *tmatrix_ptr = NULL; + + if(matrix){ + + #ifdef _HAVE_PETSC_ + PetscMatrixToDoubleMatrix(&matrix_ptr,&rows,&cols,matrix->matrix); + #else + matrix_ptr=matrix->matrix->ToSerial(); + matrix->matrix->GetSize(&rows,&cols); + #endif + + /*Now transpose the matrix and allocate with Matlab's memory manager: */ + tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); + for(i=0;ivector); + #else + vector_ptr=vector->vector->ToMPISerial(); + vector->vector->GetSize(&rows); + #endif + + /*now create the matlab vector with Matlab's memory manager */ + vector_matlab=(double*)mxMalloc(rows*sizeof(double)); + for(int i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../objects/objects.h" +#include "../../Container/Container.h" +#include "../../include/include.h" + +#include + +void WriteData(mxArray** pdataref,Matrix* matrix); +void WriteData(mxArray** pdataref,double* matrix, int M,int N); +void WriteData(mxArray** pdataref,int* matrix, int M,int N); +void WriteData(mxArray** pdataref,Vector* vector); +void WriteData(mxArray** pdataref,double* vector, int M); +void WriteData(mxArray** pdataref,int integer); +void WriteData(mxArray** pdataref,bool boolean); +void WriteData(mxArray** pdataref,double scalar); +void WriteData(mxArray** pdataref,char* string); +void WriteData(mxArray** pdataref,BamgGeom* bamggeom); +void WriteData(mxArray** pdataref,BamgMesh* bamgmesh); + +void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(Matrix** pmatrix,const mxArray* dataref); +void FetchData(int** pvector,int* pM,const mxArray* dataref); +void FetchData(float** pvector,int* pM,const mxArray* dataref); +void FetchData(double** pvector,int* pM,const mxArray* dataref); +void FetchData(bool** pvector,int* pM,const mxArray* dataref); +void FetchData(Vector** pvector,const mxArray* dataref); +void FetchData(char** pstring,const mxArray* dataref); +void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(double* pscalar,const mxArray* dataref); +void FetchData(int* pinteger,const mxArray* dataref); +void FetchData(bool* pbool,const mxArray* dataref); +void FetchData(BamgGeom** bamggeom,const mxArray* dataref); +void FetchData(BamgMesh** bamgmesh,const mxArray* dataref); +void FetchData(BamgOpts** bamgopts,const mxArray* dataref); +void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref); + +Option* OptionParse(char* name, const mxArray* prhs[]); +OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]); +OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]); +OptionChar* OptionCharParse( char* name, const mxArray* prhs[]); +OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]); +OptionCell* OptionCellParse( char* name, const mxArray* prhs[]); + +mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number, const char* field); +void SetStructureField(mxArray* dataref,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void )); + +/*Matlab to Matrix routines: */ +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); +Vector* MatlabVectorToVector(const mxArray* mxvector); + +/*Matlab to double* routines: */ +int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); +int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); +int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + +/*Matlab to SeqMat routines: */ +SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); +SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); + +/*Matlab to Petsc routines: */ +#ifdef _HAVE_PETSC_ +int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); +int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); +#endif + + +#endif /* _IO_H_ */ Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/mxGetAssignedField.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/mxGetAssignedField.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/mxGetAssignedField.cpp (revision 12168) @@ -0,0 +1,45 @@ +/*!\file: mxGetAssignedField.c: + * \brief: abstract interface on parallel side for i/o, so it ressembles the serial i/o. + * + * In serial mode, this routine takes care of returning the field coming + * from the model. If largesize is 1, we are running out of core models in + * matlab, and we need to call the subsref private method from the model object + * in order to correctly load the data from disk. + */ + +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "mex.h" + +mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){ + + //output + mxArray* mxfield=NULL; + + //input + mxArray *inputs[2]; + mxArray *pindex = NULL; + const char *fnames[2]; + mwSize ndim = 2; + mwSize onebyone[2] = {1,1}; + + //We want to call the subsasgn method, and get the returned array.This ensures that if we are running + //large sized problems, the data is truly loaded from disk by the model subsasgn class method. + inputs[0]=(mxArray*)pmxa_array; //this is the model + + //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex) + fnames[0] = "type"; + fnames[1] = "subs"; + pindex=mxCreateStructArray( ndim,onebyone,2,fnames); + mxSetField( pindex, 0, "type",mxCreateString(".")); + mxSetField( pindex, 0, "subs",mxCreateString(field)); + inputs[1]=pindex; + + mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref"); + + return mxfield; +} Index: /issm/branches/trunk-jpl-damage/src/c/matlab/matlab-binding.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/matlab-binding.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/matlab-binding.h (revision 12168) @@ -0,0 +1,7 @@ +#ifndef _MATLAB_BINDING_H_ +#define _MATLAB_BINDING_H_ + +#include "./io/matlabio.h" +#include "./include/matlab_macros.h" + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12168) @@ -32,5 +32,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -95,5 +95,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); @@ -135,5 +135,5 @@ /*Is there just one found? that would mean we have frozen! : */ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -195,5 +195,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -228,5 +228,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -289,5 +289,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); @@ -329,5 +329,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&max_penetration,&mpi_max_penetration,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_max_penetration,1,MPI_DOUBLE,0,MPI_COMM_WORLD); @@ -368,5 +368,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12168) @@ -36,5 +36,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12168) @@ -28,5 +28,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12168) @@ -11,5 +11,5 @@ #include "./ContourToMeshx.h" -int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { +int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue) { int noerr=1; @@ -37,5 +37,4 @@ /*initialize thread parameters: */ - gate.numcontours=numcontours; gate.contours=contours; gate.nods=nods; Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12168) @@ -13,6 +13,5 @@ typedef struct{ - int numcontours; - Contour** contours; + DataSet* contours; int nods; int edgevalue; @@ -25,5 +24,5 @@ /* local prototypes: */ -int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); +int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue); void* ContourToMeshxt(void* vContourToMeshxThreadStruct); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12168) @@ -26,13 +26,7 @@ /*Contour:*/ - Contour* contouri=NULL; - int numnodes; - double* xc=NULL; - double* yc=NULL; - + DataSet* contours=NULL; /*parameters: */ - int numcontours; - Contour** contours=NULL; int nods; int edgevalue; @@ -49,5 +43,4 @@ /*recover parameters :*/ - numcontours=gate->numcontours; contours=gate->contours; nods=gate->nods; @@ -61,10 +54,7 @@ /*Loop through all contours: */ - for (i=0;inods; - xc=contouri->x; - yc=contouri->y; - IsInPoly(in_nod,xc,yc,numnodes,x,y,i0,i1,edgevalue); + for (i=0;iSize();i++){ + Contour* contour=(Contour*)contours->GetObjectByOffset(i); + IsInPoly(in_nod,contour->x,contour->y,contour->nods,x,y,i0,i1,edgevalue); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 12168) @@ -38,2 +38,36 @@ return 1; } + +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue){ + + int i; + int m,n; + + /*Contour:*/ + Contour* contouri=NULL; + int numnodes; + double* xc=NULL; + double* yc=NULL; + double value; + + /*output: */ + Vector* flags=NULL; + + flags=new Vector(nods); + + /*Loop through all contours: */ + if(contours){ + for (i=0;iSize();i++){ + Contour* contour=(Contour*)contours->GetObjectByOffset(i); + IsInPoly(flags,contour->x,contour->y,contour->nods,x,y,0,nods,edgevalue); + } + } + + /*Assemble vector: */ + flags->Assemble(); + + /*Assign output pointers: */ + *pflags=flags; + + return 1; +} Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 12168) @@ -12,4 +12,5 @@ /* local prototypes: */ int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue); #endif /* _CONTOURTONODESX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.cpp (revision 12168) @@ -51,9 +51,5 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Dakotax(mxArray* femmodel){ -#else void Dakotax(FemModel* femmodel){ -#endif @@ -69,9 +65,5 @@ /*Retrieve parameters: */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - FetchData((Parameters**)¶meters,mxGetField((mxArray*)femmodel,0,"parameters")); - #else parameters=femmodel->parameters; - #endif /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ @@ -80,15 +72,9 @@ parameters->FindParam(&dakota_error_file,QmuErrNameEnum); - #ifdef _PARALLEL_ if(my_rank==0){ - #endif // Instantiate/initialize the parallel library and problem description // database objects. - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - Dakota::ParallelLibrary parallel_lib; //use Dakota's standard library mode constructor - #else - Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. - #endif + Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. Dakota::ProblemDescDB problem_db(parallel_lib); @@ -123,10 +109,7 @@ selected_strategy.run_strategy(); - #ifdef _PARALLEL_ //Warn other cpus that we are done running the dakota iterator, by setting the counter to -1: SpawnCore(NULL,0, NULL,NULL,0,femmodel,-1); - #endif - #ifdef _PARALLEL_ } else{ @@ -136,5 +119,4 @@ } } - #endif //#ifdef _PARALLEL_ /*Free ressources:*/ @@ -143,8 +125,4 @@ xfree((void**)&dakota_output_file); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - delete parameters; - #endif - #endif //#ifdef _HAVE_DAKOTA_ } Index: /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/Dakotax.h (revision 12168) @@ -10,14 +10,9 @@ /* local prototypes: */ -int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); +int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); int DescriptorIndex(char* root, int* pindex,char* descriptor); -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Dakotax(mxArray* femmodel); -void SpawnCoreSerial(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, mxArray* femmodel,int counter); -#else void Dakotax(FemModel* femmodel); void SpawnCoreParallel(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, FemModel* femmodel,int counter); -#endif void DakotaResponses(double* responses,char** responses_descriptors,int numresponses,FemModel* femmodel); void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/SpawnCore.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/SpawnCore.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/SpawnCore.cpp (revision 12168) @@ -21,12 +21,9 @@ /*Branch into a serial SpawnCore and a parallel SpawnCore: */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - SpawnCoreSerial(responses, numresponses, variables, variables_descriptors,numvariables, (mxArray*)femmodel, counter); - #else - /*Call SpawnCoreParallel unless counter=-1 on cpu0, in which case, bail out and return 0: */ - MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); - if(counter==-1)return 0; - SpawnCoreParallel(responses, numresponses, variables, variables_descriptors,numvariables, (FemModel*)femmodel,counter); - #endif + /*Call SpawnCoreParallel unless counter=-1 on cpu0, in which case, bail out and return 0: */ + MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); + if(counter==-1)return 0; + + SpawnCoreParallel(responses, numresponses, variables, variables_descriptors,numvariables, (FemModel*)femmodel,counter); return 1; } Index: sm/branches/trunk-jpl-damage/src/c/modules/Dakotax/SpawnCoreSerial.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Dakotax/SpawnCoreSerial.cpp (revision 12167) +++ (revision ) @@ -1,71 +1,0 @@ -/*!\file: SpawnCoreSerial.cpp - * \brief: run core ISSM solution using Dakota inputs. Call the Serial core solution, using mexCallMATLAB - * \sa SpawnCore.cpp SpawnCoreParallel.cpp - * - */ - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include "../../objects/objects.h" -#include "../../io/io.h" -#include "../../EnumDefinitions/EnumDefinitions.h" -#include "../../shared/shared.h" -#include "./Dakotax.h" -#include "../../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void SpawnCoreSerial(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, mxArray* femmodel, int counter){ - - int i; - - //inputs to matlab routine - mxArray* mxvariables=NULL; - double* variables_copy=NULL; - mxArray* mxvariabledescriptors=NULL; - mxArray* mxcounter=NULL; - mwSize dims[2]={0}; - - //mexCallMATLAB arrays - mxArray* array[4]; - - //output from SpawnCore in matlab routine. - mxArray* mxresponses=NULL; - - /*Create variables and variable descriptors mxArrays that we will feed to the core solution for update of the inputs: */ - mxvariables=mxCreateDoubleMatrix(numvariables,1,mxREAL); - variables_copy=(double*)xmalloc(numvariables*sizeof(double)); - memcpy(variables_copy,variables,numvariables*sizeof(double)); - mxSetPr(mxvariables,variables_copy); - - dims[0]=numvariables; - dims[1]=1; - mxvariabledescriptors=mxCreateCellArray(2,dims); - for(i=0;iAssemble(); + #ifdef _HAVE_MPI_ MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); _printf_(VerboseConvergence()," Additional number of vertices allowed to unground: %i\n",nflipped); + #else + nflipped=local_nflipped; + #endif /*Avoid leaks: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/IceVolumex/IceVolumex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12168) @@ -19,6 +19,10 @@ local_ice_volume+=element->IceVolume(); } + #ifdef _HAVE_MPI_ MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #else + total_ice_volume=local_ice_volume; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputConvergencex/InputConvergencex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12168) @@ -30,5 +30,5 @@ /*In parallel, we need to gather the converged status: */ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&num_notconverged,(void*)&total_notconverged,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); num_notconverged=total_notconverged; Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 12168) @@ -14,5 +14,5 @@ int InterpFromMeshToMesh2dx(double** pdata_interp,double* index_data,double* x_data,double* y_data,int nods_data,int nels_data, - double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values, Contour** contours, int numcontours){ + double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values, DataSet* contours){ /*Output*/ @@ -36,5 +36,4 @@ bool skip_bamg=false; - /*Checks*/ if (data_cols<=0){ @@ -50,5 +49,5 @@ /*If default values supplied, figure out which nodes are inside the contour, including the border of the contour: */ if(num_default_values){ - ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,numcontours,1); + ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,1); incontour=vec_incontour->ToMPISerial(); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 12168) @@ -10,5 +10,5 @@ /* local prototypes: */ int InterpFromMeshToMesh2dx(double** pdata_interp,double* index_data,double* x_data,double* y_data,int nods_data,int nels_data, - double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values,Contour** contours, int numcontours ); + double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values,DataSet* contours); #endif Index: /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp (revision 12168) @@ -0,0 +1,22 @@ +/*!\file: Kriging.cpp + * \brief "c" core code for Kriging + */ + +#include "./Krigingx.h" +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" +#include "../../objects/objects.h" +#include "../modules.h" + +int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp){ + + /*output*/ + double *predictions = NULL; + + /*Allocate output*/ + predictions=(double*)xmalloc(n_interp*sizeof(double)); + + /*Assign output pointer*/ + *ppredictions=predictions; +} Index: /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h (revision 12168) @@ -0,0 +1,15 @@ +/*!\file Kriging.h + * \brief: header file for Kriging + */ + +#ifndef _KRIGINGX_H +#define _KRIGINGX_H + +#include "../../objects/objects.h" +#include "../../toolkits/toolkits.h" + + +int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp); + +#endif /* _KRIGINGX_H */ + Index: /issm/branches/trunk-jpl-damage/src/c/modules/MassFluxx/MassFluxx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12168) @@ -59,5 +59,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&mass_flux,(void*)&all_mass_flux,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD); mass_flux=all_mass_flux; Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvx,&node_maxabsvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12168) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvy,&node_maxabsvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvz,&node_maxabsvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxVelx/MaxVelx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12168) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvel,&node_maxvel,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxVxx/MaxVxx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvx,&node_maxvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxVyx/MaxVyx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvy,&node_maxvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MaxVzx/MaxVzx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12168) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvz,&node_maxvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MeshPartitionx/MeshPartitionx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12168) @@ -42,5 +42,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements,&numberofnodes, index, &etype, &numflag, &num_procs, &edgecut, epart, npart); + #endif } else if (num_procs==1){ @@ -67,5 +69,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements2d,&numberofnodes2d, index2d, &etype2d, &numflag, &num_procs, &edgecut, epart2d, npart2d); + #endif } else if (num_procs==1){ Index: /issm/branches/trunk-jpl-damage/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12168) @@ -6,5 +6,5 @@ int SegmentIntersect(double* palpha, double* pbeta, double* x1, double* y1, double* x2, double* y2){ - /*See ISSM_TIER/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ + /*See ISSM_DIR/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ /*output: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/MinVelx/MinVelx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MinVelx/MinVelx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MinVelx/MinVelx.cpp (revision 12168) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvel,&node_minvel,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MinVxx/MinVxx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MinVxx/MinVxx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MinVxx/MinVxx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MinVyx/MinVyx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MinVyx/MinVyx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MinVyx/MinVyx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvy,&node_minvy,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/MinVzx/MinVzx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/MinVzx/MinVzx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/MinVzx/MinVzx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12168) @@ -63,5 +63,4 @@ else elements_width=6; //penta elements - #ifdef _PARALLEL_ /*Determine parallel partitioning of elements: we use Metis for now. First load the data, then partition*/ if(dim==2){ @@ -79,9 +78,4 @@ xfree((void**)&elements); xfree((void**)&elements2d); - - #else - /*In serial mode, epart is full of 0: all elements belong to cpu 0: */ - epart=(int*)xcalloc(numberofelements,sizeof(int)); - #endif /*Deal with rifts, they have to be included into one partition only, not several: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/NodalValuex/NodalValuex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12168) @@ -36,10 +36,16 @@ /*Broadcast whether we found the element: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); if(!sumfound)_error_("%s%i%s%s","could not find element with vertex with id",index," to compute nodal value ",EnumToStringx(natureofdataenum)); + #endif /*Broadcast and plug into response: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); MPI_Bcast(&value,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); + #else + value=cpu_found; + #endif *pnodalvalue=value; Index: /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12168) @@ -16,9 +16,5 @@ #include "../../objects/objects.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ -#else void OutputResultsx( Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ -#endif extern int my_rank; @@ -31,11 +27,4 @@ bool dakota_analysis = false; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - const char **fnames = NULL; - mwSize onebyone[2] = {0,0}; - mwSize ndim = 2; - int nfields=0; - #endif - /*retrieve parameters: */ parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); @@ -43,7 +32,4 @@ if(dakota_analysis){ //no need to output anything, Dakota analysis has different outputs - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - *pdataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); - #endif return; } @@ -56,5 +42,4 @@ /*Results do not include the type of solution being run . In parallel, we output results to a filename, *therefore, we need to include the solutiontype into the filename: */ - #ifdef _PARALLEL_ if(my_rank==0){ parameters->FindParam(&solutiontype,SolutionTypeEnum); @@ -88,26 +73,19 @@ parameters->SetParam(fid,OutputFilePointerEnum); } - #endif - /*Write results to disk (in parallel), or to memory (in serial mode): */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - results->Write(pdataref); - #else - results->Write(parameters); - #endif + /*Write results to disk: */ + results->Write(parameters); /*Delete and reinitialize results, in parallel: */ - #ifdef _PARALLEL_ - results->clear(); + results->clear(); - /*Close output file? :*/ - /*WARNING: issm.cpp is taking care of it for now (quick fix) - if((step==1) && (time==0)){ - if(io_gather){ - if(my_rank==0) pfclose(fid,outputfilename); - } - else pfclose(fid,cpu_outputfilename); - } - */ - #endif + /*Close output file? :*/ + /*WARNING: issm.cpp is taking care of it for now (quick fix) + if((step==1) && (time==0)){ + if(io_gather){ + if(my_rank==0) pfclose(fid,outputfilename); + } + else pfclose(fid,cpu_outputfilename); + } + */ } Index: /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12168) @@ -14,10 +14,5 @@ #include "../../Container/Container.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); -#else void OutputResultsx(Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); -#endif #endif /* _OUTPUTRESULTS_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12168) @@ -92,6 +92,6 @@ } - #ifdef _PARALLEL_ /*Ok, broadcast to other cpus: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&numanalyses,1,MPI_INT,0,MPI_COMM_WORLD); if(my_rank!=0){ @@ -100,4 +100,5 @@ } MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif for(i=0;iSize();i++){ - element=(Element*)elements->GetObjectByOffset(i); - element->PositiveDegreeDay(); - } +// void PositiveDegreeDayx(hd,vTempsea,vPrec,agd,Tsurf,ni){ +// note "v" prefix means 12 monthly means, ie time dimension +// INPUT parameters: ni: working size of arrays +// INPUT: surface elevation (m): hd(NA) +// monthly mean surface sealevel temperature (degrees C): vTempsea(NA +// ,NTIME) +// monthly mean precip rate (m/yr water equivalent): vPrec(NA,NTIME) +// OUTPUT: mass-balance (m/yr ice): agd(NA) +// mean annual surface temperature (degrees C): Tsurf(NA) + int i, it, jj, itm; + double DT = 0.02, sigfac, snormfac; + double signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day + double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm + double signormc; // sigma of the temperature distribution for cloudy day + double siglimc=0, siglim0, siglim0c; + double tstep, tsint, tint, tstepc; + int NPDMAX = 1504, NPDCMAX = 1454; + //double pdds[NPDMAX]={0}; + //double pds[NPDCMAX]={0}; + double pddt, pd ; // pd : snow/precip fraction, precipitation falling as snow + double PDup, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) + double tstar; // monthly mean surface temp + + double* pdds=NULL; + double* pds=NULL; + Element* element = NULL; + + pdds=(double*)xmalloc(NPDMAX*sizeof(double)+1); + pds=(double*)xmalloc(NPDCMAX*sizeof(double)+1); + + + // PDD constant + siglim = 2.5*signorm; + + // initialize PDD (creation of a lookup table) + tstep = 0.1; + tsint = tstep*0.5; + sigfac = -1.0/(2.0*pow(signorm,2)); + snormfac = 1.0/(signorm*sqrt(2.0*acos(-1.0))); + siglim = 2.5*signorm; + itm = (int)(2*siglim/DT + 1.5); + + if (itm >= NPDMAX){ + printf("increase NPDMAX in massBalance.cpp\n"); + exit (1); + } + for (it = 0; it < itm; it++){ + // tstar = REAL(it)*DT-siglim; + tstar = it*DT-siglim; + tint = tsint; + pddt = 0; + for ( jj = 0; jj < 600; jj++){ + if (tint > (tstar+siglim)){break;} + pddt = pddt + tint*exp(sigfac*(pow((tint-tstar),2)))*tstep; + tint = tint+tstep; + } + pdds[it] = pddt*snormfac; + } + pdds[itm+1] = siglim + DT; + + //*********compute PD(T) : snow/precip fraction. precipitation falling as snow + tstepc = 0.1; + tsint = PDCUT-tstepc*0.5; + signormc = signorm - 0.5; + sigfac = -1.0/(2.0*pow(signormc,2)); + snormfac = 1.0/(signormc*sqrt(2.0*acos(-1.0))); + siglimc = 2.5*signormc ; + itm = (int)((PDCUT+2.*siglimc)/DT + 1.5); + if (itm >= NPDCMAX){ + printf("'increase NPDCMAX in p35com'\n"); + exit (1); + } + for (it = 0; it < itm; it++ ){ + tstar = it*DT-siglimc; + // tstar = REAL(it)*DT-siglimc; + tint = tsint; // start against upper bound + pd = 0; + for (jj = 0; jj < 600; jj++){ + if (tint<(tstar-siglimc)) {break;} + pd = pd + exp(sigfac*(pow((tint-tstar),2)))*tstepc; + tint = tint-tstepc; + } + pds[it] = pd*snormfac; // gaussian integral lookup table for snow fraction + } + pds[itm+1] = 0; + // *******END initialize PDD + + for(i=0;iSize();i++){ + element=(Element*)elements->GetObjectByOffset(i); + element->PositiveDegreeDay(pdds,pds,signorm); + } + /*free ressouces: */ + xfree((void**)&pdds); + xfree((void**)&pds); + } Index: /issm/branches/trunk-jpl-damage/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 12168) @@ -34,8 +34,4 @@ /*In serial mode, the Petsc Options database has not been initialized properly: */ - #ifdef _SERIAL_ - parameters->FindParam(&analysis_type,AnalysisTypeEnum); - PetscOptionsFromAnalysis(parameters,analysis_type); - #endif SolverxPetsc(&uf_vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12168) @@ -43,5 +43,4 @@ #endif - /*Display message*/ _printf_(VerboseModule()," Solving\n"); @@ -52,5 +51,5 @@ #endif - /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ + /*First, check that f-set is not NULL, i.e. model is fully constrained:*/ _assert_(Kff); MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); @@ -58,6 +57,6 @@ *puf=NULL; return; } - /*}}}*/ - /*Initial guess logic here: {{{1*/ + + /*Initial guess */ /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ #if _PETSC_MAJOR_ >= 3 @@ -74,54 +73,23 @@ MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); } - /*}}}*/ - /*Process petsc options to see if we are using special types of external solvers: {{{1*/ + + /*Process petsc options to see if we are using special types of external solvers*/ PetscOptionsDetermineSolverType(&solver_type); - /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. - We need to convert them if we are going to run the solvers successfully: */ - #ifdef _SERIAL_ - #if _PETSC_MAJOR_ == 2 - if (solver_type==MUMPSPACKAGE_LU){ - /*Convert Kff to MATTAIJMUMPS: */ - MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + /*Check the solver is available*/ + if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ + #if _PETSC_MAJOR_ >=3 + #ifndef _HAVE_MUMPS_ + _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); + #endif + #endif } - if (solver_type==MUMPSPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_LU){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SUPERLUDISTPACKAGE){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==StokesSolverEnum){ - _error_("Petsc 2 does not support multi-physics solvers"); - } - #endif - #endif - /*}}}*/ - /*Check the solver is available: {{{1*/ - if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ - #if _PETSC_MAJOR_ >=3 - #ifndef _HAVE_MUMPS_ - _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); - #endif - #endif - } - /*}}}*/ - /*Prepare solver:{{{1*/ + /*Prepare solver*/ KSPCreate(MPI_COMM_WORLD,&ksp); KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); KSPSetFromOptions(ksp); - #if defined(_SERIAL_) && _PETSC_MAJOR_==3 + #if _PETSC_MAJOR_==3 /*Specific solver?: */ KSPGetPC(ksp,&pc); @@ -133,7 +101,5 @@ #endif } - #endif - #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 /*Stokes: */ if (solver_type==StokesSolverEnum){ @@ -155,16 +121,15 @@ #endif - /*}}}*/ - /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ + /*If there is an initial guess for the solution, use it + * except if we are using the MUMPS direct solver + * where any initial guess will crash Petsc*/ if (uf0){ - if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ + if((solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); } } - /*}}}*/ - - if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); /*Solve: */ + if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); KSPSolve(ksp,pf,uf); Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAreax/SurfaceAreax.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12168) @@ -28,7 +28,9 @@ /*Sum all J from all cpus of the cluster:*/ - MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + #ifdef _HAVE_MPI_ + MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&S_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); S=S_sum; + #endif /*add surface area to element inputs:*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12168) @@ -31,7 +31,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12168) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/TimeAdaptx/TimeAdaptx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12168) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&min_dt,&node_min_dt,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_min_dt,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/branches/trunk-jpl-damage/src/c/modules/TriMeshx/TriMeshx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12168) @@ -10,8 +10,15 @@ #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" +/*ANSI_DECLARATORS needed to call triangle library: */ +#ifndef ANSI_DECLARATORS +#define ANSI_DECLARATORS +#include "triangle.h" +#undef ANSI_DECLARATORS +#else +#include "triangle.h" +#endif /*}}}*/ - -void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,double area,bool order){ +void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ /*indexing: */ @@ -28,5 +35,5 @@ /*intermediary: */ - int counter,backcounter; + int counter,counter2,backcounter; Contour* contour=NULL; @@ -39,6 +46,11 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); + in.numberofpoints+=contour->nods-1; + } + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); in.numberofpoints+=contour->nods; } + /*number of point attributes: */ in.numberofpointattributes=1; @@ -50,4 +62,12 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); + for (j=0;jnods-1;j++){ + in.pointlist[2*counter+0]=contour->x[j]; + in.pointlist[2*counter+1]=contour->y[j]; + counter++; + } + } + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); for (j=0;jnods;j++){ in.pointlist[2*counter+0]=contour->x[j]; @@ -58,5 +78,5 @@ /*fill in the point attribute list: */ - in.pointattributelist = (REAL *) xmalloc(in.numberofpoints * in.numberofpointattributes * sizeof(REAL)); + in.pointattributelist = (REAL*)xmalloc(in.numberofpoints*in.numberofpointattributes*sizeof(REAL)); for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); - in.numberofsegments+=contour->nods; + in.numberofsegments+=contour->nods-1; + } + for(i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); + /*for rifts, we have one less segment as we have vertices*/ + in.numberofsegments+=contour->nods-1; } @@ -79,5 +103,5 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); - for (j=0;jnods-1;j++){ + for (j=0;jnods-2;j++){ in.segmentlist[2*counter+0]=counter; in.segmentlist[2*counter+1]=counter+1; @@ -92,5 +116,16 @@ backcounter=counter; } - + counter2=counter; + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); + for (j=0;j<(contour->nods-1);j++){ + in.segmentlist[2*counter2+0]=counter; + in.segmentlist[2*counter2+1]=counter+1; + in.segmentmarkerlist[counter2]=2+i; + counter2++; + counter++; + } + counter++; + } /*Build regions: */ @@ -103,20 +138,19 @@ for (i=0;iSize()-1;i++){ contour=(Contour*)domain->GetObjectByOffset(i+1); - GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods,contour->x,contour->y); + GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods-1,contour->x,contour->y); } } /* Make necessary initializations so that Triangle can return a triangulation in `out': */ - - out.pointlist = (REAL *) NULL; - out.pointattributelist = (REAL *) NULL; - out.pointmarkerlist = (int *) NULL; - out.trianglelist = (int *) NULL; - out.triangleattributelist = (REAL *) NULL; - out.neighborlist = (int *) NULL; - out.segmentlist = (int *) NULL; - out.segmentmarkerlist = (int *) NULL; - out.edgelist = (int *) NULL; - out.edgemarkerlist = (int *) NULL; + out.pointlist = (REAL*)NULL; + out.pointattributelist = (REAL*)NULL; + out.pointmarkerlist = (int *)NULL; + out.trianglelist = (int *)NULL; + out.triangleattributelist = (REAL*)NULL; + out.neighborlist = (int *)NULL; + out.segmentlist = (int *)NULL; + out.segmentmarkerlist = (int *)NULL; + out.edgelist = (int *)NULL; + out.edgemarkerlist = (int *)NULL; /* Triangulate the points:. Switches are chosen to read and write a */ @@ -125,12 +159,7 @@ /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ /* neighbor list (n). */ - sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/ - - triangulate(options, &in, &out, NULL); - /*report(&out, 0, 1, 1, 1, 1, 0);*/ - /*Allocate index, x and y: */ @@ -141,15 +170,14 @@ segmentmarkerlist=(double*)xmalloc(out.numberofsegments*sizeof(double)); - for (i = 0; i < out.numberoftriangles; i++) { + for (i = 0; i< out.numberoftriangles; i++) { for (j = 0; j < out.numberofcorners; j++) { - *(index+3*i+j)=(double)out.trianglelist[i * out.numberofcorners + j]+1; - } - } - for (i = 0; i < out.numberofpoints; i++) { - x[i]=out.pointlist[i * 2 + 0]; - y[i]=out.pointlist[i * 2 + 1]; - } - - for (i = 0; i < out.numberofsegments; i++) { + index[3*i+j]=(double)out.trianglelist[i*out.numberofcorners+j]+1; + } + } + for (i = 0; i< out.numberofpoints; i++){ + x[i]=out.pointlist[i*2+0]; + y[i]=out.pointlist[i*2+1]; + } + for (i = 0; iVertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); - FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); - this->TangentAtEdgesSize[0]=0, this->TangentAtEdgesSize[1]=0; this->TangentAtEdges=NULL; - FetchData(&this->Corners, &this->CornersSize[0], &this->CornersSize[1], mxGetAssignedField(matlab_struct,0,"Corners")); - FetchData(&this->RequiredVertices,&this->RequiredVerticesSize[0],&this->RequiredVerticesSize[1],mxGetAssignedField(matlab_struct,0,"RequiredVertices")); - FetchData(&this->RequiredEdges, &this->RequiredEdgesSize[0], &this->RequiredEdgesSize[1], mxGetAssignedField(matlab_struct,0,"RequiredEdges")); - FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); - FetchData(&this->SubDomains, &this->SubDomainsSize[0], &this->SubDomainsSize[1], mxGetAssignedField(matlab_struct,0,"SubDomains")); - -} -#endif -/*}}}*/ /*FUNCTION BamgGeom::~BamgGeom(){{{1*/ BamgGeom::~BamgGeom(){ @@ -49,77 +33,2 @@ } /*}}}*/ - -/*Methods*/ -/*FUNCTION BamgGeom::SetMatlabStructureFields{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgGeom::SetMatlabStructureFields(mxArray** matlab_struct){ - - /*Intermediary*/ - int i; - mxArray* output=NULL; - const int numfields=7; - const char* fnames[numfields]; - mwSize ndim=2; - mwSize dimensions[2]={1,1}; - - /*Initialize field names*/ - i=0; - fnames[i++] = "Vertices"; - fnames[i++] = "Edges"; - fnames[i++] = "TangentAtEdges"; - fnames[i++] = "RequiredVertices"; - fnames[i++] = "RequiredEdges"; - fnames[i++] = "CrackedEdges"; - fnames[i++] = "SubDomains"; - _assert_(i==numfields); - - /*Initialize Matlab structure*/ - output=mxCreateStructArray(ndim,dimensions,numfields,fnames); - - /*set each matlab each field*/ - i=0; - i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); - i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); - i++; SetMatlabStructureField(output,"TangentAtEdges", this->TangentAtEdgesSize[0], this->TangentAtEdgesSize[1], this->TangentAtEdges); - i++; SetMatlabStructureField(output,"RequiredVertices",this->RequiredVerticesSize[0],this->RequiredVerticesSize[1],this->RequiredVertices); - i++; SetMatlabStructureField(output,"RequiredEdges", this->RequiredEdgesSize[0], this->RequiredEdgesSize[1], this->RequiredEdges); - i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); - i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); - _assert_(i==numfields); - - /*Assign output*/ - *matlab_struct=output; - -} -#endif -/*}}}*/ -/*FUNCTION BamgGeom::SetMatlabStructureField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgGeom::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ - - /*Intermediary*/ - int i1,i2; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - - /*Copy field*/ - double* fieldcopy=NULL; - if (fieldrows*fieldcols){ - fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); - for(i1=0;i1 -#endif class BamgGeom{ @@ -30,13 +26,5 @@ BamgGeom(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgGeom(mxArray* matlab_struct); - #endif ~BamgGeom(); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabStructureFields(mxArray** matlab_struct); - void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); - #endif }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgMesh.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgMesh.cpp (revision 12168) @@ -18,7 +18,7 @@ this->CrackedEdgesSize[0]=0, this->CrackedEdgesSize[1]=0; this->CrackedEdges=NULL; - this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0;this->VerticesOnGeomVertex=NULL; - this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; - this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; + this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0; this->VerticesOnGeomVertex=NULL; + this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; + this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; @@ -28,37 +28,5 @@ this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; - - } -/*}}}*/ -/*FUNCTION BamgMesh::BamgMesh(mxArray* matlab_struct){{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -BamgMesh::BamgMesh(mxArray* matlab_struct){ - - int lines,cols; - - FetchData(&this->Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); - FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); - FetchData(&this->Triangles, &this->TrianglesSize[0], &this->TrianglesSize[1], mxGetAssignedField(matlab_struct,0,"Triangles")); - this->QuadrilateralsSize[0]=0, this->QuadrilateralsSize[1]=0; this->Quadrilaterals=NULL; - - this->SubDomainsSize[0]=0, this->SubDomainsSize[1]=0; this->SubDomains=NULL; - this->SubDomainsFromGeomSize[0]=0, this->SubDomainsFromGeomSize[1]=0; this->SubDomainsFromGeom=NULL; - this->CrackedVerticesSize[0]=0, this->CrackedVerticesSize[1]=0; this->CrackedVertices=NULL; - FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); - - FetchData(&this->VerticesOnGeomEdge, &this->VerticesOnGeomEdgeSize[0], &this->VerticesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"VerticesOnGeomEdge")); - FetchData(&this->VerticesOnGeomVertex,&this->VerticesOnGeomVertexSize[0],&this->VerticesOnGeomVertexSize[1],mxGetAssignedField(matlab_struct,0,"VerticesOnGeomVertex")); - FetchData(&this->EdgesOnGeomEdge, &this->EdgesOnGeomEdgeSize[0], &this->EdgesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"EdgesOnGeomEdge")); - - this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; - FetchData(&this->IssmSegments, &this->IssmSegmentsSize[0], &this->IssmSegmentsSize[1], mxGetAssignedField(matlab_struct,0,"IssmSegments")); - - this->ElementConnectivitySize[0]=0, this->ElementConnectivitySize[1]=0; this->ElementConnectivity=NULL; - this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; - this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; - -} -#endif /*}}}*/ /*FUNCTION BamgMesh::~BamgMesh(){{{1*/ @@ -89,95 +57,2 @@ } /*}}}*/ - -/*Methods*/ -/*FUNCTION BamgMesh::SetMatlabStructureFields{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgMesh::SetMatlabStructureFields(mxArray** matlab_struct){ - - /*Intermediary*/ - int i; - mxArray* output=NULL; - const int numfields=16; - const char* fnames[numfields]; - mwSize ndim=2; - mwSize dimensions[2]={1,1}; - - /*Initialize field names*/ - i=0; - fnames[i++] = "Triangles"; - fnames[i++] = "Vertices"; - fnames[i++] = "Edges"; - fnames[i++] = "IssmSegments"; - fnames[i++] = "IssmEdges"; - fnames[i++] = "Quadrilaterals"; - fnames[i++] = "VerticesOnGeomVertex"; - fnames[i++] = "VerticesOnGeomEdge"; - fnames[i++] = "EdgesOnGeomEdge"; - fnames[i++] = "SubDomains"; - fnames[i++] = "SubDomainsFromGeom"; - fnames[i++] = "ElementConnectivity"; - fnames[i++] = "NodalConnectivity"; - fnames[i++] = "NodalElementConnectivity"; - fnames[i++] = "CrackedVertices"; - fnames[i++] = "CrackedEdges"; - _assert_(i==numfields); - - /*Initialize Matlab structure*/ - output=mxCreateStructArray(ndim,dimensions,numfields,fnames); - - /*set each matlab each field*/ - i=0; - i++; SetMatlabStructureField(output,"Triangles", this->TrianglesSize[0], this->TrianglesSize[1], this->Triangles); - i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); - i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); - i++; SetMatlabStructureField(output,"IssmSegments", this->IssmSegmentsSize[0], this->IssmSegmentsSize[1], this->IssmSegments); - i++; SetMatlabStructureField(output,"IssmEdges", this->IssmEdgesSize[0], this->IssmEdgesSize[1], this->IssmEdges); - i++; SetMatlabStructureField(output,"Quadrilaterals", this->QuadrilateralsSize[0], this->QuadrilateralsSize[1], this->Quadrilaterals); - i++; SetMatlabStructureField(output,"VerticesOnGeomVertex",this->VerticesOnGeomVertexSize[0],this->VerticesOnGeomVertexSize[1], this->VerticesOnGeomVertex); - i++; SetMatlabStructureField(output,"VerticesOnGeomEdge", this->VerticesOnGeomEdgeSize[0], this->VerticesOnGeomEdgeSize[1], this->VerticesOnGeomEdge); - i++; SetMatlabStructureField(output,"EdgesOnGeomEdge", this->EdgesOnGeomEdgeSize[0], this->EdgesOnGeomEdgeSize[1], this->EdgesOnGeomEdge); - i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); - i++; SetMatlabStructureField(output,"SubDomainsFromGeom", this->SubDomainsFromGeomSize[0], this->SubDomainsFromGeomSize[1], this->SubDomainsFromGeom); - i++; SetMatlabStructureField(output,"ElementConnectivity", this->ElementConnectivitySize[0], this->ElementConnectivitySize[1], this->ElementConnectivity); - i++; SetMatlabStructureField(output,"NodalConnectivity", this->NodalConnectivitySize[0], this->NodalConnectivitySize[1], this->NodalConnectivity); - i++; SetMatlabStructureField(output,"NodalElementConnectivity", this->NodalElementConnectivitySize[0], this->NodalElementConnectivitySize[1], this->NodalElementConnectivity); - i++; SetMatlabStructureField(output,"CrackedVertices", this->CrackedVerticesSize[0], this->CrackedVerticesSize[1], this->CrackedVertices); - i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); - _assert_(i==numfields); - - /*Assign output*/ - *matlab_struct=output; - -} -#endif -/*}}}*/ -/*FUNCTION BamgMesh::SetMatlabStructureField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgMesh::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ - - /*Intermediary*/ - int i1,i2; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - - /*Copy field*/ - double* fieldcopy=NULL; - if (fieldrows*fieldcols){ - fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); - for(i1=0;i1 -#endif class BamgMesh{ @@ -51,14 +47,5 @@ BamgMesh(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgMesh(mxArray* matlab_struct); - #endif ~BamgMesh(); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabStructureFields(mxArray** matlab_struct); - void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); - #endif - }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.cpp (revision 12168) @@ -40,44 +40,4 @@ } -/*}}}*/ -/*FUNCTION BamgOpts::BamgOpts(mxArray* matlab_struct){{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -BamgOpts::BamgOpts(mxArray* matlab_struct){ - - FetchData(&this->anisomax,mxGetField(matlab_struct,0,"anisomax")); - FetchData(&this->cutoff,mxGetField(matlab_struct,0,"cutoff")); - FetchData(&this->coeff,mxGetField(matlab_struct,0,"coeff")); - FetchData(&this->errg,mxGetField(matlab_struct,0,"errg")); - FetchData(&this->gradation,mxGetField(matlab_struct,0,"gradation")); - FetchData(&this->Hessiantype,mxGetField(matlab_struct,0,"Hessiantype")); - FetchData(&this->MaxCornerAngle,mxGetField(matlab_struct,0,"MaxCornerAngle")); - FetchData(&this->maxnbv,mxGetField(matlab_struct,0,"maxnbv")); - FetchData(&this->maxsubdiv,mxGetField(matlab_struct,0,"maxsubdiv")); - FetchData(&this->Metrictype,mxGetField(matlab_struct,0,"Metrictype")); - FetchData(&this->nbjacobi,mxGetField(matlab_struct,0,"nbjacobi")); - FetchData(&this->nbsmooth,mxGetField(matlab_struct,0,"nbsmooth")); - FetchData(&this->omega,mxGetField(matlab_struct,0,"omega")); - FetchData(&this->power,mxGetField(matlab_struct,0,"power")); - FetchData(&this->verbose,mxGetField(matlab_struct,0,"verbose")); - - FetchData(&this->Crack,mxGetField(matlab_struct,0,"Crack")); - FetchData(&this->geometricalmetric,mxGetField(matlab_struct,0,"geometricalmetric")); - FetchData(&this->KeepVertices,mxGetField(matlab_struct,0,"KeepVertices")); - FetchData(&this->splitcorners,mxGetField(matlab_struct,0,"splitcorners")); - - FetchData(&this->hmin,mxGetField(matlab_struct,0,"hmin")); - FetchData(&this->hmax,mxGetField(matlab_struct,0,"hmax")); - FetchData(&this->hminVertices,&this->hminVerticesSize[0],&this->hminVerticesSize[1],mxGetField(matlab_struct,0,"hminVertices")); - FetchData(&this->hmaxVertices,&this->hmaxVerticesSize[0],&this->hmaxVerticesSize[1],mxGetField(matlab_struct,0,"hmaxVertices")); - FetchData(&this->hVertices,&this->hVerticesSize[0],&this->hVerticesSize[1],mxGetField(matlab_struct,0,"hVertices")); - FetchData(&this->metric,&this->metricSize[0],&this->metricSize[1],mxGetField(matlab_struct,0,"metric")); - FetchData(&this->field,&this->fieldSize[0],&this->fieldSize[1],mxGetField(matlab_struct,0,"field")); - FetchData(&this->err,&this->errSize[0],&this->errSize[1],mxGetField(matlab_struct,0,"err")); - - /*Additional checks*/ - this->Check(); - -} -#endif /*}}}*/ /*FUNCTION BamgOpts::~BamgOpts() {{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgOpts.h (revision 12168) @@ -5,8 +5,4 @@ #ifndef _BAMGOPTS_H_ #define _BAMGOPTS_H_ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif class BamgOpts{ @@ -54,7 +50,4 @@ BamgOpts(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgOpts(mxArray* matlab_struct); - #endif ~BamgOpts(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Metric.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Metric.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Metric.h (revision 12168) @@ -5,4 +5,5 @@ #include "../../shared/Bamg/shared.h" #include "R2.h" +#include namespace bamg { Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.h (revision 12168) @@ -33,9 +33,4 @@ int Id(){_error_("not implemented yet");}; int MyRank(){_error_("not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("not implemented yet");}; - int MarshallSize(){_error_("not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("not implemented yet");}; - #endif int ObjectEnum(){_error_("not implemented yet");}; Object* copy(){_error_("not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.cpp (revision 12168) @@ -72,68 +72,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcDynamic::Marshall {{{1*/ -void SpcDynamic::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcDynamic: */ - enum_type=SpcDynamicEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcDynamic data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&isset,sizeof(isset));marshalled_dataset+=sizeof(isset); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcDynamic::MarshallSize {{{1*/ -int SpcDynamic::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(value) - +sizeof(isset) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcDynamic::Demarshall {{{1*/ -void SpcDynamic::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&isset,marshalled_dataset,sizeof(isset));marshalled_dataset+=sizeof(isset); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcDynamic::ObjectEnum{{{1*/ int SpcDynamic::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcDynamic.h (revision 12168) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.cpp (revision 12168) @@ -75,65 +75,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcStatic::Marshall {{{1*/ -void SpcStatic::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcStatic: */ - enum_type=SpcStaticEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcStatic data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcStatic::MarshallSize {{{1*/ -int SpcStatic::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(value) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcStatic::Demarshall {{{1*/ -void SpcStatic::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcStatic::ObjectEnum{{{1*/ int SpcStatic::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcStatic.h (revision 12168) @@ -33,9 +33,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.cpp (revision 12168) @@ -87,76 +87,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcTransient::Marshall {{{1*/ -void SpcTransient::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcTransient: */ - enum_type=SpcTransientEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcTransient data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&nsteps,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - if(nsteps){ - memcpy(marshalled_dataset,values,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - memcpy(marshalled_dataset,times,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - } - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcTransient::MarshallSize {{{1*/ -int SpcTransient::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(nsteps) - +nsteps*2*sizeof(double) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcTransient::Demarshall {{{1*/ -void SpcTransient::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&nsteps,marshalled_dataset,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - if(nsteps){ - values=(double*)xmalloc(nsteps*sizeof(double)); - times=(double*)xmalloc(nsteps*sizeof(double)); - memcpy(values,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - memcpy(times,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcTransient::ObjectEnum{{{1*/ int SpcTransient::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/SpcTransient.h (revision 12168) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Contour.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Contour.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Contour.cpp (revision 12168) @@ -79,71 +79,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Contour::Marshall{{{1*/ -void Contour::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputssize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Contour: */ - enum_type=ContourEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Contour data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&nods,sizeof(nods));marshalled_dataset+=sizeof(nods); - memcpy(marshalled_dataset,&closed,sizeof(closed));marshalled_dataset+=sizeof(closed); - memcpy(marshalled_dataset,x,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - memcpy(marshalled_dataset,y,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Contour::MarshallSize{{{1*/ -int Contour::MarshallSize(){ - - return sizeof(id)+ - sizeof(nods)+ - sizeof(closed)+ - 2*nods*sizeof(double)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Contour::Demarshall{{{1*/ -void Contour::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&nods,marshalled_dataset,sizeof(nods));marshalled_dataset+=sizeof(nods); - memcpy(&closed,marshalled_dataset,sizeof(closed));marshalled_dataset+=sizeof(closed); - - if(nods){ - this->x=(double*)xmalloc(nods*sizeof(double)); - this->y=(double*)xmalloc(nods*sizeof(double)); - memcpy(x,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - memcpy(y,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Contour::ObjectEnum{{{1*/ int Contour::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Contour.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Contour.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Contour.h (revision 12168) @@ -34,9 +34,4 @@ int Id(void); int MyRank(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(void); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(void); Object* copy(void); Index: /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.cpp (revision 12168) @@ -208,128 +208,3 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DofIndexing::Marshall{{{1*/ -void DofIndexing::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - bool flagdoftype; //to indicate if there are some doftype or if NULL - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*preliminary: */ - if(this->doftype)flagdoftype=true; - else flagdoftype=false; - - /*get enum type of DofIndexing: */ - enum_type=DofIndexingEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall DofIndexing data: */ - memcpy(marshalled_dataset,&gsize,sizeof(gsize));marshalled_dataset+=sizeof(gsize); - memcpy(marshalled_dataset,&fsize,sizeof(fsize));marshalled_dataset+=sizeof(fsize); - memcpy(marshalled_dataset,&ssize,sizeof(ssize));marshalled_dataset+=sizeof(ssize); - memcpy(marshalled_dataset,&flagdoftype,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); - memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); - - if(this->gsize>0){ - memcpy(marshalled_dataset,f_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(marshalled_dataset,s_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(marshalled_dataset,svalues,gsize*sizeof(double)); marshalled_dataset+=gsize*sizeof(double); - if(flagdoftype){ memcpy(marshalled_dataset,doftype,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); } - memcpy(marshalled_dataset,gdoflist,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); - } - if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(marshalled_dataset,fdoflist,fsize*sizeof(int)); marshalled_dataset+=fsize*sizeof(int);} - if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(marshalled_dataset,sdoflist,ssize*sizeof(int)); marshalled_dataset+=ssize*sizeof(int);} - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION DofIndexing::MarshallSize{{{1*/ -int DofIndexing::MarshallSize(){ - - int size=0; - - size+=4*sizeof(int)+sizeof(bool); - if(this->gsize>0){ - size+= 2*this->gsize*sizeof(bool)+ - this->gsize*sizeof(double)+ - this->gsize*sizeof(int); - if(this->doftype)size+=this->gsize*sizeof(int); - } - if(this->fsize>0 && this->fsize!=UNDEF)size+=this->fsize*sizeof(int); - if(this->ssize>0 && this->ssize!=UNDEF)size+=this->ssize*sizeof(int); - - size+=sizeof(int); //sizeof(int) for enum type - - return size; -} -/*}}}*/ -/*FUNCTION DofIndexing::Demarshall{{{1*/ -void DofIndexing::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type; - bool flagdoftype; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of object since DofIndexing is not directly called by DataSet: */ - memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - - /*easy part: */ - memcpy(&gsize,marshalled_dataset,sizeof(gsize));marshalled_dataset+=sizeof(gsize); - memcpy(&fsize,marshalled_dataset,sizeof(fsize));marshalled_dataset+=sizeof(fsize); - memcpy(&ssize,marshalled_dataset,sizeof(ssize));marshalled_dataset+=sizeof(ssize); - memcpy(&flagdoftype,marshalled_dataset,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); - memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); - - /*Allocate: */ - if(this->gsize>0){ - this->f_set=(bool*)xmalloc(this->gsize*sizeof(bool)); - this->s_set=(bool*)xmalloc(this->gsize*sizeof(bool)); - this->svalues=(double*)xmalloc(this->gsize*sizeof(double)); - if(flagdoftype)this->doftype=(int*)xmalloc(this->gsize*sizeof(int)); - else this->doftype=NULL; - this->gdoflist=(int*)xmalloc(this->gsize*sizeof(int)); - } - else{ - this->f_set=NULL; - this->s_set=NULL; - this->svalues=NULL; - this->doftype=NULL; - this->gdoflist=NULL; - } - if(this->fsize>0) - this->fdoflist=(int*)xmalloc(this->fsize*sizeof(int)); - else - this->fdoflist=NULL; - if(this->ssize>0) - this->sdoflist=(int*)xmalloc(this->ssize*sizeof(int)); - else - this->sdoflist=NULL; - - /*Copy arrays: */ - if(this->gsize>0){ - memcpy(f_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(s_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(svalues,marshalled_dataset,gsize*sizeof(double));marshalled_dataset+=gsize*sizeof(double); - if(flagdoftype){memcpy(doftype,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); } - memcpy(gdoflist,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); - } - - if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(this->fdoflist,marshalled_dataset,this->fsize*sizeof(int));marshalled_dataset+=this->fsize*sizeof(int); } - if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(this->sdoflist,marshalled_dataset,this->ssize*sizeof(int));marshalled_dataset+=this->ssize*sizeof(int); } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif - + Index: /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/DofIndexing.h (revision 12168) @@ -43,9 +43,4 @@ void Echo(void); void DeepEcho(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif void copy(DofIndexing* properties); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12168) @@ -64,61 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolElementResult::Marshall{{{1*/ -void BoolElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolElementResult: */ - enum_value=BoolElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolElementResult::Demarshall{{{1*/ -void BoolElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION BoolElementResult::MarshallSize{{{1*/ -int BoolElementResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -#endif /*FUNCTION BoolElementResult::ObjectEnum{{{1*/ int BoolElementResult::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h (revision 12168) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12168) @@ -64,61 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleElementResult::Marshall{{{1*/ -void DoubleElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleElementResult: */ - enum_value=DoubleElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleElementResult::Demarshall{{{1*/ -void DoubleElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION DoubleElementResult::MarshallSize{{{1*/ -int DoubleElementResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -#endif /*FUNCTION DoubleElementResult::ObjectEnum{{{1*/ int DoubleElementResult::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h (revision 12168) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12168) @@ -67,61 +67,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PentaP1ElementResult::Marshall{{{1*/ -void PentaP1ElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PentaP1ElementResult: */ - enum_value=PentaP1ElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PentaP1ElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PentaP1ElementResult::MarshallSize{{{1*/ -int PentaP1ElementResult::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PentaP1ElementResult::Demarshall{{{1*/ -void PentaP1ElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION PentaP1ElementResult::ObjectEnum{{{1*/ int PentaP1ElementResult::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12168) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12168) @@ -66,62 +66,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TriaP1ElementResult::Marshall{{{1*/ -void TriaP1ElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TriaP1ElementResult: */ - enum_value=TriaP1ElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TriaP1ElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION TriaP1ElementResult::MarshallSize{{{1*/ -int TriaP1ElementResult::MarshallSize(){ - - return sizeof(values) - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TriaP1ElementResult::Demarshall{{{1*/ -void TriaP1ElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION TriaP1ElementResult::ObjectEnum{{{1*/ int TriaP1ElementResult::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12168) @@ -33,9 +33,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 12168) @@ -71,5 +71,5 @@ virtual void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding)=0; virtual void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding)=0; - virtual void PositiveDegreeDay(void)=0; + virtual void PositiveDegreeDay(double* pdds,double* pds,double signorm)=0; virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; virtual void ResetCoordinateSystem()=0; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 12168) @@ -142,161 +142,4 @@ } /*}}}*/ - -/*Marshall*/ -#ifdef _SERIAL_ -/*FUNCTION Penta::Marshall {{{1*/ -void Penta::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - char* marshalled_results=NULL; - int marshalled_results_size; - int flaghook; //to indicate if hook is NULL or exists - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Penta: */ - enum_type=PentaEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Penta data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*Mershall Ref: */ - for(i=0;iMarshall(&marshalled_dataset); - } - else{ - /*Set flag to 0 and do not marshall flag as there is no Hook */ - flaghook=0; - memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); - } - } - hmatice->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - hneighbors->Marshall(&marshalled_dataset); - - /*Marshall inputs and results: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - marshalled_results_size=results->MarshallSize(); - marshalled_results=results->Marshall(); - memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); - marshalled_dataset+=marshalled_results_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - xfree((void**)&marshalled_results); - - /*marshall horizontal neighbors: */ - memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Penta::MarshallSize {{{1*/ -int Penta::MarshallSize(){ - - int i; - int hnodes_size=0;; - - for(i=0;iMarshallSize(); - } - - return sizeof(id) - +sizeof(sid) - +hnodes_size - +sizeof(numanalyses) - +numanalyses*sizeof(int) //element_type_lists - +hmatice->MarshallSize() - +hmatpar->MarshallSize() - +hneighbors->MarshallSize() - +inputs->MarshallSize() - +results->MarshallSize() - +3*sizeof(int) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Penta::Demarshall {{{1*/ -void Penta::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int flaghook; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*demarshall Ref: */ - this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); - for(i=0;ihnodes=new Hook*[this->numanalyses]; - /*demarshall hooks: */ - for(i=0;iDemarshall(&marshalled_dataset); - } - else hnodes[i]=NULL; //There is no hook so it is NULL - } - hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - hneighbors=new Hook(); hneighbors->Demarshall(&marshalled_dataset); - - /*pointers are garbage, until configuration is carried out: */ - nodes=NULL; - matice=NULL; - matpar=NULL; - verticalneighbors=NULL; - - /*demarshall inputs and results: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*neighbors: */ - memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*Other*/ @@ -2421,7 +2264,225 @@ /*}}}*/ /*FUNCTION Penta::PositiveDegreeDay{{{1*/ -void Penta::PositiveDegreeDay(){ - - _error_("Not implemented yet"); +void Penta::PositiveDegreeDay(double* pdds,double* pds,double signorm){ + + + int i,iqj,imonth; + double agd[NUMVERTICES]; // surface and basal + double saccu[NUMVERTICES] = {0}; // yearly surface accumulation + double smelt[NUMVERTICES] = {0}; // yearly melt + double precrunoff[NUMVERTICES]; // yearly runoff + double prect; // total precipitation during 1 year taking into account des. ef. + double water; //water=rain + snowmelt + double runoff; //meltwater only, does not include rain + double sconv; //rhow_rain/rhoi / 12 months + + double rho_water,rho_ice,density; + double lapser=6.5/1000, sealev=0; // lapse rate. degrees per meter. + double desfac = 0.5; //desert elevation factor + double s0p[NUMVERTICES]={0}; //should be set to elevation from precip source + double s0t[NUMVERTICES]={0}; //should be set to elevation from temperature source + double st; // elevation between altitude of the temp record and current altitude + double sp; // elevation between altitude of the prec record and current altitude + + + // PDD and PD constants and variables + double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm + double siglimc=0, siglim0, siglim0c; + double PDup, pddsig, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) + double DT = 0.02; + double pddt, pd; // pd: snow/precip fraction, precipitation falling as snow + + double q, qmpt; // q is desert/elev. fact, hnpfac is huybrect fact, and pd is normal dist. + double qm[NUMVERTICES] = {0}; // snow part of the precipitation + double qmt[NUMVERTICES] = {0}; // precipitation without desertification effect adjustment + double qmp[NUMVERTICES] = {0}; // desertification taken into account + double pdd[NUMVERTICES] = {0}; + double frzndd[NUMVERTICES] = {0}; + + double tstar; // monthly mean surface temp + double Tsum[NUMVERTICES]= {0}; // average summer (JJA) temperature + double Tsurf[NUMVERTICES] = {0}; // average annual temperature + + double h[NUMVERTICES],s[NUMVERTICES],ttmp[NUMVERTICES],prectmp[NUMVERTICES]; // ,b[NUMVERTICES] + double t[NUMVERTICES][12],prec[NUMVERTICES][12]; + double deltm=1/12; + int ismon[12]={12,1,2,3,4,5,6,7,8,9,10,11}; + + double snwm; // snow that could have been melted in a year. + double snwmf; // ablation factor for snow per positive degree day. + double smf; // ablation factor for ice per pdd (Braithwaite 1995 from tarasov 2002). + + double dfrz=1.5, CovrLm=2009./3.35e+5, dCovrLm=dfrz*CovrLm; //m*J kg^-1 C^-1 /(J kg^-1)=m/C yr + double supice,supcap,diffndd; + double fsupT=0.5, fsupndd=0.5; // Tsurf mode factors for supice + double pddtj[NUMVERTICES], hmx2; + + /*Recover info at the vertices: */ + GetInputListOnVertices(&h[0],ThicknessEnum); + GetInputListOnVertices(&s[0],SurfaceEnum); + GetInputListOnVertices(&ttmp[0],ThermalSpctemperatureEnum); + GetInputListOnVertices(&prectmp[0],SurfaceforcingsPrecipitationEnum); + + for(i=0;iGetRhoIce(); + rho_water=matpar->GetRhoWater(); + density=rho_ice/rho_water; + + sconv=(rho_water/rho_ice)/12.; //rhow_rain/rhoi / 12 months + + /*PDD constant*/ + siglim = 2.5*signorm; + siglim0 = siglim/DT + 0.5; + siglim0c = siglimc/DT + 0.5; + PDup = siglimc+PDCUT; + + // seasonal loop + for (iqj = 0; iqj < 12; iqj++){ + imonth = ismon[iqj]; + for (i = 0; i < NUMVERTICES; i++){ + st=(s[i]-s0t[i])/1000; + tstar = t[i][imonth] - lapser *max(st,sealev); + Tsurf[i] = tstar*deltm+Tsurf[i]; + + /*********compute PD ****************/ + if (tstar < PDup){ + pd = 1; + if (tstar >= -siglimc){ pd = pds[int(tstar/DT + siglim0c)];}} + else { + pd = 0;} + + /******exp des/elev precip reduction*******/ + sp=(s[i]-s0p[i])/1000; // deselev effect is wrt chng in topo + if (sp>0.0){q = exp(-desfac*sp);} + else {q = 1.0;} + + qmt[i]= qmt[i] + prec[i][imonth]*sconv; //*sconv to convert in m of ice equivalent + qmpt= q*prec[i][imonth]*sconv; + qmp[i]= qmp[i] + qmpt; + qm[i]= qm[i] + qmpt*pd; + + /*********compute PDD************/ + // ndd(month)=-(tstar-pdd(month)) since ndd+pdd gives expectation of + // gaussian=T_m, so ndd=-(Tsurf-pdd) + if (iqj>6 && iqj<10){ Tsum[i]=Tsum[i]+tstar;} + if (tstar >= siglim) {pdd[i] = pdd[i] + tstar*deltm;} + else if (tstar> -siglim){ + pddsig=pdds[int(tstar/DT + siglim0)]; + pdd[i] = pdd[i] + pddsig*deltm; + frzndd[i] = frzndd[i] - (tstar-pddsig)*deltm;} + else{frzndd[i] = frzndd[i] - tstar*deltm; } + } + } // end of seasonal loop + + //****************************************************************** + for(i=0;i2m) + // problem with water seepage into ice: should be sealed after + // refreezing + // so everything needs to be predicated on 1 year scale, except for + // thermal + // conductivity through ice + // also, need to account that melt season has low accum, so what's + // going to + // hold the meltwater around for refreezing? And melt-time will have + // low seasonal frzndd + + // Superimposed ice : Pfeffer et al. 1991, Tarasov 2002 + + supice= min(hmx2*CovrLm*frzndd[i]+2.2*(saccu[i]-snwm), water); // superimposed ice + supcap=min(2.2*(saccu[i]-snwm),water); + runoff=snwm - supice; //meltwater only, does not include rain + } + else { //all snow melted + supice= min(hmx2*CovrLm*frzndd[i], prect ); + runoff= saccu[i] + smf*(pddt-saccu[i]/snwmf) - supice; + supcap=0; + } + // pdd melting doesn't cool Tsurf, so ndd refreeze shouldn't warm it + // except pdd melt heat source is atmosphere, while refreeze is + // ground/ice stored interim + // assume pdd=ndd, then melt should equal refreeze and Tsurf should=0 + // assume ndd=2*pdd, then all supice is refrozen, but Tsurf should be + // <0 + // assume ndd>pdd, little melt => little supice + // bottom line: compare for Tsurf<0 : supice and no supice case, + // expect Tsurf difference + // except some of cooling flux comes from atmosphere// + // 1 dm supice should not raise Tsurf by 1/dCovrLm = 16.675C + // does supice make sense when H< 0.1m? then d=thermoactive ice layer //// + // < 0.1 + + // make more sense to just use residual pdd-ndd except that pdd + // residual not clear yet + // frzndd should not be used up by refreezing in snow, so stick in + // supcap. + diffndd=0; + if (frzndd[i]>0) { + diffndd=fsupndd*min((supice-supcap)/dCovrLm ,frzndd[i]); + frzndd[i]=frzndd[i]-diffndd; + } + if(runoff<0){ + saccu[i]= saccu[i] -runoff; + smelt[i] = 0; + precrunoff[i]=prect-saccu[i]; + //here assume pdd residual is 0, => + Tsurf[i]= max(Tsurf[i],-frzndd[i]); + } + else { + smelt[i] = runoff; + precrunoff[i]=prect-max(0.,supice)-saccu[i];} + //here really need pdd balance, try 0.5 fudge factor? + //at least runoff>0 => it's fairly warm, so Tsurf is !<<0, + //yet from site plots, can be ice free with Tsurf=-5.5C + if(Tsurf[i]<0) { + Tsurf[i]= min(Tsurf[i]+fsupT*diffndd , 0.);} + + agd[i] = -smelt[i]+saccu[i]; + pddtj[i]=pddt; + + /*Update inputs*/ + this->inputs->AddInput(new PentaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0])); ////////verifier le nom + // this->inputs->AddInput(new TriaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0])); + this->inputs->AddInput(new PentaP1Input(ThermalSpctemperatureEnum,&Tsurf[0])); + + } //end of the for loop over the vertices } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 12168) @@ -55,9 +55,4 @@ int ObjectEnum(); int Id(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int MyRank(); /*}}}*/ @@ -112,5 +107,5 @@ void PatchFill(int* pcount, Patch* patch); void PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes); - void PositiveDegreeDay(void); + void PositiveDegreeDay(double* pdds,double* pds,double signorm); void ProcessResultsUnits(void); void ResetCoordinateSystem(void); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 12168) @@ -122,158 +122,4 @@ } /*}}}*/ - -/*Marshall*/ -#ifdef _SERIAL_ -/*FUNCTION Tria::Marshall {{{1*/ -void Tria::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - char* marshalled_results=NULL; - int marshalled_results_size; - int flaghook; //to indicate if hook is NULL or exists - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Tria: */ - enum_type=TriaEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Tria data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*Mershall Ref: */ - for(i=0;iMarshall(&marshalled_dataset); - } - else{ - /*Set flag to 0 and do not marshall flag as there is no Hook */ - flaghook=0; - memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); - } - } - hmatice->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*Marshall results: */ - marshalled_results_size=results->MarshallSize(); - marshalled_results=results->Marshall(); - memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); - marshalled_dataset+=marshalled_results_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - xfree((void**)&marshalled_results); - - /*marshall horizontal neighbors: */ - memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Tria::MarshallSize {{{1*/ -int Tria::MarshallSize(){ - - int i; - int hnodes_size=0;; - - for(i=0;iMarshallSize(); - } - - return sizeof(id) - +sizeof(sid) - +hnodes_size - +sizeof(numanalyses) - +numanalyses*sizeof(int) //element_type_lists - +hmatice->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +results->MarshallSize() - +3*sizeof(int) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Tria::Demarshall {{{1*/ -void Tria::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int flaghook; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*demarshall Ref: */ - this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); - for(i=0;ihnodes=new Hook*[this->numanalyses]; - /*demarshall hooks: */ - for(i=0;iDemarshall(&marshalled_dataset); - } - else hnodes[i]=NULL; //There is no hook so it is NULL - } - hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - matice=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*neighbors: */ - memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*Other*/ @@ -2241,7 +2087,224 @@ /*}}}*/ /*FUNCTION Tria::PositiveDegreeDay{{{1*/ -void Tria::PositiveDegreeDay(){ - - _error_("Not implemented yet"); +void Tria::PositiveDegreeDay(double* pdds,double* pds,double signorm){ + + int i,iqj,imonth; + double agd[NUMVERTICES]; // surface and basal + double saccu[NUMVERTICES] = {0}; // yearly surface accumulation + double smelt[NUMVERTICES] = {0}; // yearly melt + double precrunoff[NUMVERTICES]; // yearly runoff + double prect; // total precipitation during 1 year taking into account des. ef. + double water; //water=rain + snowmelt + double runoff; //meltwater only, does not include rain + double sconv; //rhow_rain/rhoi / 12 months + + double rho_water,rho_ice,density; + double lapser=6.5/1000, sealev=0; // lapse rate. degrees per meter. + double desfac = 0.5; //desert elevation factor + double s0p[NUMVERTICES]={0}; //should be set to elevation from precip source + double s0t[NUMVERTICES]={0}; //should be set to elevation from temperature source + double st; // elevation between altitude of the temp record and current altitude + double sp; // elevation between altitude of the prec record and current altitude + + + // PDD and PD constants and variables + double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm + double siglimc=0, siglim0, siglim0c; + double PDup, pddsig, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) + double DT = 0.02; + double pddt, pd; // pd: snow/precip fraction, precipitation falling as snow + + double q, qmpt; // q is desert/elev. fact, hnpfac is huybrect fact, and pd is normal dist. + double qm[NUMVERTICES] = {0}; // snow part of the precipitation + double qmt[NUMVERTICES] = {0}; // precipitation without desertification effect adjustment + double qmp[NUMVERTICES] = {0}; // desertification taken into account + double pdd[NUMVERTICES] = {0}; + double frzndd[NUMVERTICES] = {0}; + + double tstar; // monthly mean surface temp + double Tsum[NUMVERTICES]= {0}; // average summer (JJA) temperature + double Tsurf[NUMVERTICES] = {0}; // average annual temperature + + double h[NUMVERTICES],s[NUMVERTICES],ttmp[NUMVERTICES],prectmp[NUMVERTICES]; // ,b[NUMVERTICES] + double t[NUMVERTICES][12],prec[NUMVERTICES][12]; + double deltm=1/12; + int ismon[12]={12,1,2,3,4,5,6,7,8,9,10,11}; + + double snwm; // snow that could have been melted in a year. + double snwmf; // ablation factor for snow per positive degree day. + double smf; // ablation factor for ice per pdd (Braithwaite 1995 from tarasov 2002). + + double dfrz=1.5, CovrLm=2009./3.35e+5, dCovrLm=dfrz*CovrLm; //m*J kg^-1 C^-1 /(J kg^-1)=m/C yr + double supice,supcap,diffndd; + double fsupT=0.5, fsupndd=0.5; // Tsurf mode factors for supice + double pddtj[NUMVERTICES], hmx2; + + /*Recover info at the vertices: */ + GetInputListOnVertices(&h[0],ThicknessEnum); + GetInputListOnVertices(&s[0],SurfaceEnum); + GetInputListOnVertices(&ttmp[0],ThermalSpctemperatureEnum); + GetInputListOnVertices(&prectmp[0],SurfaceforcingsPrecipitationEnum); + + for(i=0;iGetRhoIce(); + rho_water=matpar->GetRhoWater(); + density=rho_ice/rho_water; + + sconv=(rho_water/rho_ice)/12.; //rhow_rain/rhoi / 12 months + + /*PDD constant*/ + siglim = 2.5*signorm; + siglim0 = siglim/DT + 0.5; + siglim0c = siglimc/DT + 0.5; + PDup = siglimc+PDCUT; + + // seasonal loop + for (iqj = 0; iqj < 12; iqj++){ + imonth = ismon[iqj]; + for (i = 0; i < NUMVERTICES; i++){ + st=(s[i]-s0t[i])/1000; + tstar = t[i][imonth] - lapser *max(st,sealev); + Tsurf[i] = tstar*deltm+Tsurf[i]; + + /*********compute PD ****************/ + if (tstar < PDup){ + pd = 1; + if (tstar >= -siglimc){ pd = pds[int(tstar/DT + siglim0c)];}} + else { + pd = 0;} + + /******exp des/elev precip reduction*******/ + sp=(s[i]-s0p[i])/1000; // deselev effect is wrt chng in topo + if (sp>0.0){q = exp(-desfac*sp);} + else {q = 1.0;} + + qmt[i]= qmt[i] + prec[i][imonth]*sconv; //*sconv to convert in m of ice equivalent + qmpt= q*prec[i][imonth]*sconv; + qmp[i]= qmp[i] + qmpt; + qm[i]= qm[i] + qmpt*pd; + + /*********compute PDD************/ + // ndd(month)=-(tstar-pdd(month)) since ndd+pdd gives expectation of + // gaussian=T_m, so ndd=-(Tsurf-pdd) + if (iqj>6 && iqj<10){ Tsum[i]=Tsum[i]+tstar;} + if (tstar >= siglim) {pdd[i] = pdd[i] + tstar*deltm;} + else if (tstar> -siglim){ + pddsig=pdds[int(tstar/DT + siglim0)]; + pdd[i] = pdd[i] + pddsig*deltm; + frzndd[i] = frzndd[i] - (tstar-pddsig)*deltm;} + else{frzndd[i] = frzndd[i] - tstar*deltm; } + } + } // end of seasonal loop + + //****************************************************************** + for(i=0;i2m) + // problem with water seepage into ice: should be sealed after + // refreezing + // so everything needs to be predicated on 1 year scale, except for + // thermal + // conductivity through ice + // also, need to account that melt season has low accum, so what's + // going to + // hold the meltwater around for refreezing? And melt-time will have + // low seasonal frzndd + + // Superimposed ice : Pfeffer et al. 1991, Tarasov 2002 + + supice= min(hmx2*CovrLm*frzndd[i]+2.2*(saccu[i]-snwm), water); // superimposed ice + supcap=min(2.2*(saccu[i]-snwm),water); + runoff=snwm - supice; //meltwater only, does not include rain + } + else { //all snow melted + supice= min(hmx2*CovrLm*frzndd[i], prect ); + runoff= saccu[i] + smf*(pddt-saccu[i]/snwmf) - supice; + supcap=0; + } + // pdd melting doesn't cool Tsurf, so ndd refreeze shouldn't warm it + // except pdd melt heat source is atmosphere, while refreeze is + // ground/ice stored interim + // assume pdd=ndd, then melt should equal refreeze and Tsurf should=0 + // assume ndd=2*pdd, then all supice is refrozen, but Tsurf should be + // <0 + // assume ndd>pdd, little melt => little supice + // bottom line: compare for Tsurf<0 : supice and no supice case, + // expect Tsurf difference + // except some of cooling flux comes from atmosphere// + // 1 dm supice should not raise Tsurf by 1/dCovrLm = 16.675C + // does supice make sense when H< 0.1m? then d=thermoactive ice layer //// + // < 0.1 + + // make more sense to just use residual pdd-ndd except that pdd + // residual not clear yet + // frzndd should not be used up by refreezing in snow, so stick in + // supcap. + diffndd=0; + if (frzndd[i]>0) { + diffndd=fsupndd*min((supice-supcap)/dCovrLm ,frzndd[i]); + frzndd[i]=frzndd[i]-diffndd; + } + if(runoff<0){ + saccu[i]= saccu[i] -runoff; + smelt[i] = 0; + precrunoff[i]=prect-saccu[i]; + //here assume pdd residual is 0, => + Tsurf[i]= max(Tsurf[i],-frzndd[i]); + } + else { + smelt[i] = runoff; + precrunoff[i]=prect-max(0.,supice)-saccu[i];} + //here really need pdd balance, try 0.5 fudge factor? + //at least runoff>0 => it's fairly warm, so Tsurf is !<<0, + //yet from site plots, can be ice free with Tsurf=-5.5C + if(Tsurf[i]<0) { + Tsurf[i]= min(Tsurf[i]+fsupT*diffndd , 0.);} + + agd[i] = -smelt[i]+saccu[i]; + pddtj[i]=pddt; + + /*Update inputs*/ + this->inputs->AddInput(new TriaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0])); ////////verifier le nom + // this->inputs->AddInput(new TriaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0])); + this->inputs->AddInput(new TriaP1Input(ThermalSpctemperatureEnum,&Tsurf[0])); + + } //end of the for loop over the vertices } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 12168) @@ -51,9 +51,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -108,5 +103,5 @@ int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); - void PositiveDegreeDay(void); + void PositiveDegreeDay(double* pdds,double* pds,double signorm); void RequestedOutput(int output_enum,int step,double time); void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12168) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolExternalResult::Marshall{{{1*/ -void BoolExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolExternalResult: */ - enum_value=BoolExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolExternalResult::MarshallSize{{{1*/ -int BoolExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolExternalResult::Demarshall{{{1*/ -void BoolExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolExternalResult::ObjectEnum{{{1*/ int BoolExternalResult::ObjectEnum(void){ @@ -185,17 +125,4 @@ } /*}}}*/ -/*FUNCTION BoolExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BoolExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar((double)value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); -} -#endif -/*}}}*/ /*FUNCTION BoolExternalResult::GetStep{{{1*/ int BoolExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12168) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -47,9 +42,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -59,9 +49,6 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ }; -#endif /* _BOOLEXTERNALRESULT_H */ +#endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12168) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleExternalResult::Marshall{{{1*/ -void DoubleExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleExternalResult: */ - enum_value=DoubleExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleExternalResult::MarshallSize{{{1*/ -int DoubleExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleExternalResult::Demarshall{{{1*/ -void DoubleExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleExternalResult::ObjectEnum{{{1*/ int DoubleExternalResult::ObjectEnum(void){ @@ -181,17 +121,4 @@ } /*}}}*/ -/*FUNCTION DoubleExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - mxSetField( dataref,this->step-1, name,mxCreateDoubleScalar(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION DoubleExternalResult::GetStep{{{1*/ int DoubleExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12168) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -48,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +51,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12168) @@ -96,73 +96,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatExternalResult::Marshall{{{1*/ -void DoubleMatExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatExternalResult: */ - enum_value=DoubleMatExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatExternalResult::MarshallSize{{{1*/ -int DoubleMatExternalResult::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleMatExternalResult::Demarshall{{{1*/ -void DoubleMatExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - values=(double*)xmalloc(M*N*sizeof(double)); - memcpy(values,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatExternalResult::ObjectEnum{{{1*/ int DoubleMatExternalResult::ObjectEnum(void){ @@ -222,37 +153,4 @@ } /*}}}*/ -/*FUNCTION DoubleMatExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatExternalResult::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - char* name=NULL; - double* doublemat=NULL; - - /*Make a copy of the value, to be used by matlab: */ - doublemat=(double*)xmalloc(M*N*sizeof(double)); - memcpy(doublemat,values,M*N*sizeof(double)); - - /*recover name: */ - this->GetResultName(&name); - - /*create matlab matrix: */ - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,N); - mxSetN(pfield,M); - mxSetPr(pfield,doublemat); - - /*transpose the matrix, from c to matlab format */ - mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); - - /*set tranpose matrix inside the dataref structure: */ - mxSetField( dataref, this->step-1, name,pfield2); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION DoubleMatExternalResult::GetStep{{{1*/ int DoubleMatExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12168) @@ -14,9 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -49,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -61,7 +51,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12168) @@ -87,70 +87,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleVecExternalResult::Marshall{{{1*/ -void DoubleVecExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleVecExternalResult: */ - enum_value=DoubleVecExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleVecExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleVecExternalResult::MarshallSize{{{1*/ -int DoubleVecExternalResult::MarshallSize(){ - - return sizeof(M) - +M*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleVecExternalResult::Demarshall{{{1*/ -void DoubleVecExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - values=(double*)xmalloc(M*sizeof(double)); - memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleVecExternalResult::ObjectEnum{{{1*/ int DoubleVecExternalResult::ObjectEnum(void){ @@ -206,32 +140,4 @@ } /*}}}*/ -/*FUNCTION DoubleVecExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleVecExternalResult::SetMatlabField(mxArray* dataref){ - - mxArray *pfield = NULL; - double *doublemat = NULL; - char *name = NULL; - double *doublevec = NULL; - - /*Make a copy of the value, to be used by matlab: */ - doublevec=(double*)xmalloc(M*sizeof(double)); - memcpy(doublevec,values,M*sizeof(double)); - - /*recover name: */ - this->GetResultName(&name); - - /*create matlab matrix: */ - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, this->step-1, name,pfield); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); -} -#endif -/*}}}*/ /*FUNCTION DoubleVecExternalResult::GetStep{{{1*/ int DoubleVecExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12168) @@ -14,9 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/ExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/ExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/ExternalResult.h (revision 12168) @@ -16,8 +16,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "../Object.h" #include "../Node.h" @@ -33,7 +29,4 @@ virtual void WriteData(FILE* fid,bool io_gather)=0; virtual void GetResultName(char**)=0; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - virtual void SetMatlabField(mxArray* dataref)=0; - #endif virtual int GetStep(void)=0; /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12168) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntExternalResult::Marshall{{{1*/ -void IntExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntExternalResult: */ - enum_value=IntExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntExternalResult::MarshallSize{{{1*/ -int IntExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntExternalResult::Demarshall{{{1*/ -void IntExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntExternalResult::ObjectEnum{{{1*/ int IntExternalResult::ObjectEnum(void){ @@ -185,18 +125,4 @@ } /*}}}*/ -/*FUNCTION IntExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION IntExternalResult::GetStep{{{1*/ int IntExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/IntExternalResult.h (revision 12168) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -46,9 +42,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -58,7 +49,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12168) @@ -80,108 +80,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PetscVecExternalResult::Marshall{{{1*/ -void PetscVecExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M; - double* serial_value=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PetscVecExternalResult: */ - enum_value=PetscVecExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PetscVecExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - if(value){ - VecGetSize(value,&M); - VecToMPISerial(&serial_value,value); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - } - else{ - M=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - } - /*Free ressources:*/ - xfree((void**)&serial_value); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PetscVecExternalResult::MarshallSize{{{1*/ -int PetscVecExternalResult::MarshallSize(){ - - int M=0; - if(value)VecGetSize(value,&M); - - return sizeof(M)+M*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PetscVecExternalResult::Demarshall{{{1*/ -void PetscVecExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int M; - double* serial_vec=NULL; - int* idxm=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - serial_vec=(double*)xmalloc(M*sizeof(double)); - memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - - value=NewVec(M); - idxm=(int*)xmalloc(M*sizeof(int)); - for(i=0;iGetResultName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, this->step-1, name, pfield); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION PetscVecExternalResult::GetStep{{{1*/ int PetscVecExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12168) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12168) @@ -71,77 +71,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringExternalResult::Marshall{{{1*/ -void StringExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringExternalResult: */ - enum_value=StringExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - stringsize=strlen(this->value)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringExternalResult::MarshallSize{{{1*/ -int StringExternalResult::MarshallSize(){ - - int stringsize; - stringsize=strlen(this->value)+1; - - return sizeof(int)+ - +stringsize*sizeof(char) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION StringExternalResult::Demarshall{{{1*/ -void StringExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - - this->value=(char*)xmalloc(stringsize*sizeof(char)); - memcpy(value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringExternalResult::ObjectEnum{{{1*/ int StringExternalResult::ObjectEnum(void){ @@ -197,19 +124,4 @@ } /*}}}*/ -/*FUNCTION StringExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name, mxCreateString(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION StringExternalResult::GetStep{{{1*/ int StringExternalResult::GetStep(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/StringExternalResult.h (revision 12168) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp (revision 12168) @@ -22,5 +22,4 @@ /*FUNCTION FemModel::constructor {{{1*/ FemModel::FemModel(char* inputfilename, char* outputfilename, const int in_solution_type,const int* analyses,const int nummodels){ -#ifdef _PARALLEL_ /*intermediary*/ @@ -75,6 +74,4 @@ /*Add output file name to parameters: */ this->parameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename)); - -#endif } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Hook.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Hook.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Hook.cpp (revision 12168) @@ -118,91 +118,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Hook::Marshall{{{1*/ -void Hook::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Hook: */ - enum_type=HookEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Hook data: */ - memcpy(marshalled_dataset,&num,sizeof(num));marshalled_dataset+=sizeof(num); - for(i=0;iids[i],sizeof(int));marshalled_dataset+=sizeof(int); - memcpy(marshalled_dataset,&this->offsets[i],sizeof(int));marshalled_dataset+=sizeof(int); - } - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Hook::MarshallSize{{{1*/ -int Hook::MarshallSize(){ - - return - sizeof(num)+ - num*sizeof(int)+ - num*sizeof(int)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Hook::Demarshall{{{1*/ -void Hook::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int enum_type; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of object since Hook is not directly called by DataSet: */ - memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - - memcpy(&num,marshalled_dataset,sizeof(num));marshalled_dataset+=sizeof(num); - - /*allocate: */ - if (num<0){ - _error_("cannot demarshall Hook as num<=0"); - } - else if (num==0){ - this->ids=NULL; - this->offsets=NULL; - this->objects=NULL; - } - else{ - - this->ids=(int*)xmalloc(num*sizeof(int)); - this->offsets=(int*)xmalloc(num*sizeof(int)); - - /*demarshall allocated ids and offsets: */ - _assert_(num<1000); - for (i=0;iids[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - memcpy(&this->offsets[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - } - - /*nullify object pointers */ - this->objects=(Object**)xmalloc(num*sizeof(Object*)); - for (i=0;iobjects[i]=NULL; - } - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Hook::copy {{{1*/ Object* Hook::copy(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Hook.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Hook.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Hook.h (revision 12168) @@ -34,9 +34,4 @@ void Echo(void); void DeepEcho(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif Object* copy(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp (revision 12168) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolInput::Marshall{{{1*/ -void BoolInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolInput: */ - enum_value=BoolInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolInput::MarshallSize{{{1*/ -int BoolInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolInput::Demarshall{{{1*/ -void BoolInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolInput::ObjectEnum{{{1*/ int BoolInput::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h (revision 12168) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h (revision 12168) @@ -36,9 +36,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.cpp (revision 12168) @@ -61,68 +61,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DatasetInput::Marshall{{{1*/ -void DatasetInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DatasetInput: */ - enum_value=DatasetInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall enum_type: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshal inputs*/ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*clean up and assign output pointer*/ - xfree((void**)&marshalled_inputs); - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DatasetInput::MarshallSize{{{1*/ -int DatasetInput::MarshallSize(){ - - int size=0; - - size=sizeof(enum_type)+ - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum value - - return size; -} -/*}}}*/ -/*FUNCTION DatasetInput::Demarshall{{{1*/ -void DatasetInput::Demarshall(char** pmarshalled_dataset){ - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*Demarshal values*/ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DatasetInput::ObjectEnum{{{1*/ int DatasetInput::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h (revision 12168) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp (revision 12168) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleInput::Marshall{{{1*/ -void DoubleInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleInput: */ - enum_value=DoubleInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleInput::MarshallSize{{{1*/ -int DoubleInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleInput::Demarshall{{{1*/ -void DoubleInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleInput::ObjectEnum{{{1*/ int DoubleInput::ObjectEnum(void){ @@ -159,9 +108,5 @@ /*FUNCTION DoubleInput::GetInputValue(bool* pvalue) {{{1*/ void DoubleInput::GetInputValue(bool* pvalue){ -#ifdef _SERIAL_ - *pvalue=(bool)value; -#else _error_("Double input of enum %s cannot return a boolean",EnumToStringx(enum_type)); -#endif } @@ -169,9 +114,5 @@ /*FUNCTION DoubleInput::GetInputValue(int* pvalue){{{1*/ void DoubleInput::GetInputValue(int* pvalue){ -#ifdef _SERIAL_ - *pvalue=(int)value; -#else _error_("Double input of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type)); -#endif } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h (revision 12168) @@ -30,9 +30,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp (revision 12168) @@ -54,55 +54,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntInput::Marshall{{{1*/ -void IntInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntInput: */ - enum_value=IntInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntInput::MarshallSize{{{1*/ -int IntInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntInput::Demarshall{{{1*/ -void IntInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntInput::ObjectEnum{{{1*/ int IntInput::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h (revision 12168) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp (revision 12168) @@ -70,55 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PentaP1Input::Marshall{{{1*/ -void PentaP1Input::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PentaP1Input: */ - enum_value=PentaP1InputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PentaP1Input data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PentaP1Input::MarshallSize{{{1*/ -int PentaP1Input::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PentaP1Input::Demarshall{{{1*/ -void PentaP1Input::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION PentaP1Input::ObjectEnum{{{1*/ int PentaP1Input::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h (revision 12168) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp (revision 12168) @@ -114,77 +114,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TransientInput::Marshall{{{1*/ -void TransientInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TransientInput: */ - enum_value=TransientInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TransientInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&numtimesteps,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); - memcpy(marshalled_dataset,timesteps,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); - - /*marshal inputs*/ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*clean up and assign output pointer*/ - xfree((void**)&marshalled_inputs); - *pmarshalled_dataset=marshalled_dataset; - -} -/*}}}* -/*FUNCTION TransientInput::MarshallSize{{{1*/ -int TransientInput::MarshallSize(){ - - return - +sizeof(enum_type)+ - +sizeof(numtimesteps)+ - +inputs->MarshallSize() - +numtimesteps*sizeof(double)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TransientInput::Demarshall{{{1*/ -void TransientInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&numtimesteps,marshalled_dataset,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); - - /*allocate: */ - timesteps=(double*)xmalloc(numtimesteps*sizeof(double)); - memcpy(timesteps,marshalled_dataset,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); - - /*Demarshal values*/ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; - -} -/*}}}*/ -#endif /*FUNCTION TransientInput::ObjectEnum{{{1*/ int TransientInput::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h (revision 12168) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp (revision 12168) @@ -70,55 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TriaP1Input::Marshall{{{1*/ -void TriaP1Input::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TriaP1Input: */ - enum_value=TriaP1InputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TriaP1Input data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION TriaP1Input::MarshallSize{{{1*/ -int TriaP1Input::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TriaP1Input::Demarshall{{{1*/ -void TriaP1Input::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION TriaP1Input::ObjectEnum{{{1*/ int TriaP1Input::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h (revision 12168) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/IoModel.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/IoModel.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/IoModel.cpp (revision 12168) @@ -198,5 +198,7 @@ /*Ok, we have reached the end of the file. break: */ record_code=0; //0 means bailout + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell others cpus we are bailing: */ + #endif break; } @@ -207,4 +209,5 @@ fread(&record_code,sizeof(int),1,this->fid); + #ifdef _HAVE_MPI_ /*Tell other cpus what we are doing: */ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell other cpus what we are going to do: */ @@ -213,11 +216,13 @@ MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD); + #endif - switch(record_code){ case 1: /*Read the boolean and broadcast it to other cpus:*/ if(fread(&booleanint,sizeof(int),1,this->fid)!=1) _error_(" could not read boolean "); + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create BoolParam: */ @@ -228,5 +233,7 @@ /*Read the integer and broadcast it to other cpus:*/ if(fread(&integer,sizeof(int),1,this->fid)!=1) _error_(" could not read integer "); + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create IntParam: */ @@ -237,5 +244,7 @@ /*Read the scalar and broadcast it to other cpus:*/ if(fread(&scalar,sizeof(double),1,this->fid)!=1) _error_(" could not read scalar "); + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*create DoubleParam: */ @@ -246,5 +255,7 @@ /*We have to read a string from disk. First read the dimensions of the string, then the string: */ if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_(" could not read length of string "); + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ @@ -254,5 +265,7 @@ /*Read string, then broadcast: */ if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -308,4 +321,5 @@ } } //}}} + #ifdef _HAVE_MPI_ else{ //cpu ~0 {{{2 for(;;){ //wait on cpu 0 @@ -377,4 +391,5 @@ } } //}}} + #endif } /*}}}*/ @@ -399,5 +414,7 @@ if(fread(&booleanint,sizeof(int),1,fid)!=1) _error_(" could not read boolean "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*cast to bool: */ @@ -428,5 +445,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -456,5 +475,7 @@ if(fread(&scalar,sizeof(double),1,fid)!=1)_error_(" could not read scalar "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -487,5 +508,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string: */ @@ -498,5 +521,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -538,10 +563,14 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } - MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -554,5 +583,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -602,10 +633,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -617,5 +652,7 @@ if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -652,5 +689,7 @@ if(fread(&numstrings,sizeof(int),1,fid)!=1) _error_(" could not read length of string array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numstrings,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string array: */ @@ -665,5 +704,7 @@ if(fread(&string_size,sizeof(int),1,fid)!=1) _error_(" could not read length of string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ string=(char*)xmalloc((string_size+1)*sizeof(char)); @@ -674,5 +715,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -717,5 +760,7 @@ if(fread(&numrecords,sizeof(int),1,fid)!=1) _error_("could not read number of records in matrix array "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numrecords,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(numrecords){ @@ -738,10 +783,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of rows in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of columns in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -754,5 +803,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -1047,11 +1098,15 @@ } } + #ifdef _HAVE_MPI_ MPI_Bcast(&found,1,MPI_INT,0,MPI_COMM_WORLD); if(!found)_error_("%s %s ","could not find data with name",EnumToStringx(data_enum)); + #endif /*Broadcast code and vector type: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); if(record_code==5) MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers:*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp (revision 12168) @@ -163,92 +163,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Icefront::Marshall {{{1*/ -void Icefront::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Icefront: */ - enum_type=IcefrontEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Icefront data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION Icefront::MarshallSize {{{1*/ -int Icefront::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +hnodes->MarshallSize() - +helement->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Icefront::Demarshall {{{1*/ -void Icefront::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - element=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Icefront::ObjectEnum{{{1*/ int Icefront::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h (revision 12168) @@ -49,9 +49,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp (revision 12168) @@ -189,87 +189,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Numericalflux::Marshall {{{1*/ -void Numericalflux::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Numericalflux: */ - enum_type=NumericalfluxEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Numericalflux data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Numericalflux::MarshallSize{{{1*/ -int Numericalflux::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +hnodes->MarshallSize() - +helement->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Numericalflux::Demarshall {{{1*/ -void Numericalflux::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - this->element=NULL; - this->nodes=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Numericalflux::ObjectEnum{{{1*/ int Numericalflux::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h (revision 12168) @@ -45,9 +45,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp (revision 12168) @@ -132,98 +132,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Pengrid::Marshall {{{1*/ -void Pengrid::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Tria: */ - enum_type=PengridEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Tria data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(marshalled_dataset,&zigzag_counter,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); - - /*Marshall hooks: */ - hnode->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Pengrid::MarshallSize {{{1*/ -int Pengrid::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +sizeof(active) - +sizeof(zigzag_counter) - +hnode->MarshallSize() - +helement->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Pengrid::Demarshall {{{1*/ -void Pengrid::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(&zigzag_counter,marshalled_dataset,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); - - /*demarshall hooks: */ - hnode=new Hook(); hnode->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - this->node=NULL; - this->element=NULL; - this->matpar=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Pengrid::ObjectEnum{{{1*/ int Pengrid::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h (revision 12168) @@ -50,9 +50,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp (revision 12168) @@ -85,67 +85,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Penpair::Marshall {{{1*/ -void Penpair::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Penpair: */ - enum_type=PenpairEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Penpair data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks*/ - hnodes->Marshall(&marshalled_dataset); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION Penpair::MarshallSize {{{1*/ -int Penpair::MarshallSize(){ - - return sizeof(id)+ - +sizeof(analysis_type) - +hnodes->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION Penpair::Demarshall {{{1*/ -void Penpair::Demarshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION Penpair::ObjectEnum{{{1*/ int Penpair::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h (revision 12168) @@ -37,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp (revision 12168) @@ -192,123 +192,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Riftfront::Marshall {{{1*/ -void Riftfront::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Riftfront: */ - enum_type=RiftfrontEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Riftfront data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(marshalled_dataset,&normal,sizeof(normal));marshalled_dataset+=sizeof(normal); - memcpy(marshalled_dataset,&length,sizeof(length));marshalled_dataset+=sizeof(length); - memcpy(marshalled_dataset,&fraction,sizeof(fraction));marshalled_dataset+=sizeof(fraction); - memcpy(marshalled_dataset,&frozen,sizeof(frozen));marshalled_dataset+=sizeof(frozen); - memcpy(marshalled_dataset,&state,sizeof(state));marshalled_dataset+=sizeof(state); - memcpy(marshalled_dataset,&counter,sizeof(counter));marshalled_dataset+=sizeof(counter); - memcpy(marshalled_dataset,&prestable,sizeof(prestable));marshalled_dataset+=sizeof(prestable); - memcpy(marshalled_dataset,&penalty_lock,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); - memcpy(marshalled_dataset,&material_converged,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helements->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Riftfront::MarshallSize {{{1*/ -int Riftfront::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +sizeof(active) - +sizeof(normal) - +sizeof(length) - +sizeof(fraction) - +sizeof(frozen) - +sizeof(state) - +sizeof(counter) - +sizeof(prestable) - +sizeof(penalty_lock) - +sizeof(material_converged) - +hnodes->MarshallSize() - +helements->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Riftfront::Demarshall {{{1*/ -void Riftfront::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(&normal,marshalled_dataset,sizeof(normal));marshalled_dataset+=sizeof(normal); - memcpy(&length,marshalled_dataset,sizeof(length));marshalled_dataset+=sizeof(length); - memcpy(&fraction,marshalled_dataset,sizeof(fraction));marshalled_dataset+=sizeof(fraction); - memcpy(&frozen,marshalled_dataset,sizeof(frozen));marshalled_dataset+=sizeof(frozen); - memcpy(&state,marshalled_dataset,sizeof(state));marshalled_dataset+=sizeof(state); - memcpy(&counter,marshalled_dataset,sizeof(counter));marshalled_dataset+=sizeof(counter); - memcpy(&prestable,marshalled_dataset,sizeof(prestable));marshalled_dataset+=sizeof(prestable); - memcpy(&penalty_lock,marshalled_dataset,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); - memcpy(&material_converged,marshalled_dataset,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helements=new Hook(); helements->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - elements=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION Riftfront::ObjectEnum{{{1*/ int Riftfront::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h (revision 12168) @@ -57,9 +57,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp (revision 12168) @@ -88,74 +88,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Matice::Marshall {{{1*/ -void Matice::Marshall(char** pmarshalled_dataset){ - - /*Intermediaries*/ - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Matice: */ - enum_type=MaticeEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Matice data: */ - memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); - - /*Marshall hooks: */ - helement->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - *pmarshalled_dataset=marshalled_dataset; - - /*clean up and return*/ - xfree((void**)&marshalled_inputs); -} -/*}}}*/ -/*FUNCTION Matice::MarshallSize{{{1*/ -int Matice::MarshallSize(){ - - return sizeof(mid) - +helement->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Matice::Demarshall {{{1*/ -void Matice::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); - - /*demarshall hooks: */ - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Matice::ObjectEnum{{{1*/ int Matice::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h (revision 12168) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.cpp (revision 12168) @@ -102,89 +102,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Matpar::Marshall {{{1*/ -void Matpar::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Matpar: */ - enum_type=MatparEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Matpar data: */ - memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); - memcpy(marshalled_dataset,&rho_ice,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); - memcpy(marshalled_dataset,&rho_water,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); - memcpy(marshalled_dataset,&mu_water,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); - memcpy(marshalled_dataset,&heatcapacity,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); - memcpy(marshalled_dataset,&thermalconductivity,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); - memcpy(marshalled_dataset,&latentheat,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); - memcpy(marshalled_dataset,&beta,sizeof(beta));marshalled_dataset+=sizeof(beta); - memcpy(marshalled_dataset,&meltingpoint,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); - memcpy(marshalled_dataset,&referencetemperature,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); - memcpy(marshalled_dataset,&mixed_layer_capacity,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); - memcpy(marshalled_dataset,&thermal_exchange_velocity,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); - memcpy(marshalled_dataset,&g,sizeof(g));marshalled_dataset+=sizeof(g); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION Matpar::MarshallSize {{{1*/ -int Matpar::MarshallSize(){ - - return sizeof(mid)+ - sizeof(rho_ice)+ - sizeof(rho_water)+ - sizeof(mu_water)+ - sizeof(heatcapacity)+ - sizeof(thermalconductivity)+ - sizeof(latentheat)+ - sizeof(beta)+ - sizeof(meltingpoint)+ - sizeof(referencetemperature)+ - sizeof(mixed_layer_capacity)+ - sizeof(thermal_exchange_velocity)+ - sizeof(g)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION Matpar::Demarshall {{{1*/ -void Matpar::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); - memcpy(&rho_ice,marshalled_dataset,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); - memcpy(&rho_water,marshalled_dataset,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); - memcpy(&mu_water,marshalled_dataset,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); - memcpy(&heatcapacity,marshalled_dataset,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); - memcpy(&thermalconductivity,marshalled_dataset,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); - memcpy(&latentheat,marshalled_dataset,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); - memcpy(&beta,marshalled_dataset,sizeof(beta));marshalled_dataset+=sizeof(beta); - memcpy(&meltingpoint,marshalled_dataset,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); - memcpy(&referencetemperature,marshalled_dataset,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); - memcpy(&mixed_layer_capacity,marshalled_dataset,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); - memcpy(&thermal_exchange_velocity,marshalled_dataset,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); - memcpy(&g,marshalled_dataset,sizeof(g));marshalled_dataset+=sizeof(g); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION Matpar::ObjectEnum{{{1*/ int Matpar::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h (revision 12168) @@ -46,9 +46,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 12168) @@ -193,87 +193,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Node::Marshall{{{1*/ -void Node::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputssize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Node: */ - enum_type=NodeEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Node data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&coord_system,9*sizeof(double));marshalled_dataset+=9*sizeof(double); - - /*marshall objects: */ - indexing.Marshall(&marshalled_dataset); - hvertex->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputssize=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputssize*sizeof(char)); - marshalled_dataset+=marshalled_inputssize; - - /*Free ressources:*/ - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Node::MarshallSize{{{1*/ -int Node::MarshallSize(){ - - return sizeof(id)+ - sizeof(sid)+ - indexing.MarshallSize()+ - hvertex->MarshallSize()+ - inputs->MarshallSize()+ - sizeof(analysis_type)+ - 9*sizeof(double)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Node::Demarshall{{{1*/ -void Node::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&coord_system,marshalled_dataset,9*sizeof(double));marshalled_dataset+=9*sizeof(double); - - /*demarshall objects: */ - indexing.Demarshall(&marshalled_dataset); - hvertex=new Hook(); hvertex->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Node::ObjectEnum{{{1*/ int Node::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 12168) @@ -44,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(){_error_("Not implemented yet (similar to Elements)");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 12168) @@ -140,38 +140,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION Matrix::ToMatlabMatrix{{{1*/ -mxArray* Matrix::ToMatlabMatrix(void){ - - mxArray* dataref=NULL; - #ifdef _HAVE_PETSC_ - PetscMatrixToMatlabMatrix(&dataref,this->matrix); - #else - dataref=this->matrix->ToMatlabMatrix(); - #endif - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabMatrixToMatrix{{{1*/ -Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ - - int dummy; - Matrix* matrix=NULL; - - /*allocate matrix object: */ - matrix=new Matrix(); - - #ifdef _HAVE_PETSC_ - MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); - #else - matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); - #endif - - return matrix; -} -/*}}}*/ -#endif /*FUNCTION Matrix::Assemble{{{1*/ void Matrix::Assemble(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 12168) @@ -21,7 +21,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif class Vector; @@ -51,7 +48,4 @@ /*Matrix specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabMatrix(void); - #endif void Assemble(void); double Norm(NormMode norm_type); @@ -66,8 +60,4 @@ }; -/*API: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); -#endif #endif //#ifndef _MATRIX_H_ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 12168) @@ -132,38 +132,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION Vector::ToMatlabVector{{{1*/ -mxArray* Vector::ToMatlabVector(void){ - - mxArray* dataref=NULL; - #ifdef _HAVE_PETSC_ - PetscVectorToMatlabVector(&dataref,this->vector); - #else - dataref=this->vector->ToMatlabVector(); - #endif - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabVectorToVector{{{1*/ -Vector* MatlabVectorToVector(const mxArray* mxvector){ - - int dummy; - Vector* vector=NULL; - - /*allocate vector object: */ - vector=new Vector(); - - #ifdef _HAVE_PETSC_ - MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); - #else - vector->vector=MatlabVectorToSeqVec(mxvector); - #endif - - return vector; -} -/*}}}*/ -#endif /*FUNCTION Vector::Assemble{{{1*/ void Vector::Assemble(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 12168) @@ -21,8 +21,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif - /*}}}*/ @@ -54,7 +50,4 @@ /*Vector specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabVector(void); - #endif void AXPY(Vector *X, double a); void AYPX(Vector *X, double a); @@ -77,8 +70,4 @@ }; -/*API: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -Vector* MatlabVectorToVector(const mxArray* mxvector); -#endif #endif //#ifndef _VECTOR_H_ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Object.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Object.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Object.h (revision 12168) @@ -21,9 +21,4 @@ virtual int Id()=0; virtual int MyRank()=0; - #ifdef _SERIAL_ - virtual void Marshall(char** pmarshalled_dataset)=0; - virtual int MarshallSize()=0; - virtual void Demarshall(char** pmarshalled_dataset)=0; - #endif virtual int ObjectEnum()=0; virtual Object* copy()=0; Index: /issm/branches/trunk-jpl-damage/src/c/objects/OptArgs.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/OptArgs.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/OptArgs.h (revision 12168) @@ -6,19 +6,8 @@ #define _OPTARGS_H_ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -#include "mex.h" -struct OptArgs{ - char* function_name; - mxArray* femmodel; -}; - -#else - class Model; struct OptArgs{ FemModel* femmodel; }; -#endif #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/Option.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/Option.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/Option.h (revision 12168) @@ -33,9 +33,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionCell.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionCell.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionCell.h (revision 12168) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionCellEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionChar.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionChar.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionChar.h (revision 12168) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionCharEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionDouble.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionDouble.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionDouble.h (revision 12168) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionDoubleEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionLogical.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionLogical.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionLogical.h (revision 12168) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionLogicalEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionStruct.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionStruct.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Options/OptionStruct.h (revision 12168) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionStructEnum;}; Object* copy(){_error_("Not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.cpp (revision 12168) @@ -62,55 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolParam::Marshall{{{1*/ -void BoolParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolParam: */ - enum_value=BoolParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolParam::MarshallSize{{{1*/ -int BoolParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolParam::Demarshall{{{1*/ -void BoolParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolParam::ObjectEnum{{{1*/ int BoolParam::ObjectEnum(void){ @@ -134,13 +83,4 @@ } /*}}}*/ -/*FUNCTION BoolParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BoolParam::SetMatlabField(mxArray* dataref){ - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); -} -#endif -/*}}}*/ /*FUNCTION BoolParam::UnitConversion{{{1*/ void BoolParam::UnitConversion(int direction_enum){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -41,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -81,7 +72,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12168) @@ -127,111 +127,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatArrayParam::Marshall{{{1*/ -void DoubleMatArrayParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatArrayParam: */ - enum_value=DoubleMatArrayParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatArrayParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - memcpy(marshalled_dataset,mdim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - memcpy(marshalled_dataset,ndim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - for(i=0;iarray[i]; - int m=this->mdim_array[i]; - int n=this->ndim_array[i]; - memcpy(marshalled_dataset,&m,sizeof(m));marshalled_dataset+=sizeof(m); - memcpy(marshalled_dataset,&n,sizeof(n));marshalled_dataset+=sizeof(n); - if(m*n)memcpy(marshalled_dataset,matrix,m*n*sizeof(double));marshalled_dataset+=m*n*sizeof(double); - } - } - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatArrayParam::MarshallSize{{{1*/ -int DoubleMatArrayParam::MarshallSize(){ - - int size=0; - int i; - - size+=sizeof(enum_type)+ - sizeof(M)+ - M*sizeof(int)+ - M*sizeof(int); - - for(i=0;imdim_array[i]; - int n=this->ndim_array[i]; - size+=sizeof(m)+sizeof(n)+m*n*sizeof(double); - } - size+=sizeof(int); //sizeof(int) for enum value - - return size; -} -/*}}}*/ -/*FUNCTION DoubleMatArrayParam::Demarshall{{{1*/ -void DoubleMatArrayParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - double* matrix=NULL; - int m,n; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum value, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - /*data: */ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - this->mdim_array=(int*)xmalloc(M*sizeof(int)); - this->ndim_array=(int*)xmalloc(M*sizeof(int)); - memcpy(this->mdim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - memcpy(this->ndim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - - this->array=(double**)xmalloc(M*sizeof(double*)); - for(i=0;iarray[i]=matrix; - } - } - else{ - this->array=NULL; - this->mdim_array=NULL; - this->ndim_array=NULL; - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatArrayParam::ObjectEnum{{{1*/ int DoubleMatArrayParam::ObjectEnum(void){ @@ -307,44 +200,4 @@ EnumToStringx(pname,this->enum_type); } -/*}}}*/ -/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatArrayParam::SetMatlabField(mxArray* dataref){ - - int i,m,n; - double* matrix=NULL; - double* outmatrix=NULL; - char* name=NULL; - mwSize dims[2]={0}; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - mxArray* pfield3=NULL; - - this->GetParameterName(&name); - dims[0]=this->M; - dims[1]=1; - pfield=mxCreateCellArray(2,dims); - - for(i=0;iM;i++){ - matrix=this->array[i]; - m=this->mdim_array[i]; - n=this->ndim_array[i]; - outmatrix=(double*)xmalloc(m*n*sizeof(double)); - memcpy(outmatrix,matrix,m*n*sizeof(double)); - - pfield2=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield2,n); - mxSetN(pfield2,m); - mxSetPr(pfield2,outmatrix); - - //transpose the outmatrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&pfield3, 1, &pfield2, "transpose"); - - mxSetCell(pfield,i,pfield3); - } - - mxSetField( dataref, 0, name,pfield); -} -#endif /*}}}*/ /*FUNCTION DoubleMatArrayParam::SetValue(double** array, int M, int* mdim_array, int* ndim_array){{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -44,9 +40,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.cpp (revision 12168) @@ -78,64 +78,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatParam::Marshall{{{1*/ -void DoubleMatParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatParam: */ - enum_value=DoubleMatParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,value,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatParam::MarshallSize{{{1*/ -int DoubleMatParam::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleMatParam::Demarshall{{{1*/ -void DoubleMatParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - value=(double*)xmalloc(M*N*sizeof(double)); - memcpy(value,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatParam::ObjectEnum{{{1*/ int DoubleMatParam::ObjectEnum(void){ @@ -169,18 +109,5 @@ /*FUNCTION DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/ void DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - int i; - - output=(int*)xmalloc((int)(M*N*sizeof(int))); - for(i=0;ienum_type); } -/*}}}*/ -/*FUNCTION DoubleMatParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatParam::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - double* doublemat=NULL; - char* name=NULL; - - this->GetParameterName(&name); - this->GetParameterValue(&doublemat,NULL,NULL); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,N); - mxSetN(pfield,M); - mxSetPr(pfield,doublemat); - - //transpose the matrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); - mxSetField( dataref, 0, name,pfield2); -} -#endif /*}}}*/ /*FUNCTION DoubleMatParam::SetValue{{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.cpp (revision 12168) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleParam::Marshall{{{1*/ -void DoubleParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleParam: */ - enum_value=DoubleParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleParam::MarshallSize{{{1*/ -int DoubleParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleParam::Demarshall{{{1*/ -void DoubleParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleParam::ObjectEnum{{{1*/ int DoubleParam::ObjectEnum(void){ @@ -133,99 +82,31 @@ /*FUNCTION DoubleParam::GetParameterValue(int* pinteger){{{1*/ void DoubleParam::GetParameterValue(int* pinteger){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - *pinteger=(int)value; -#else _error_("Double param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(bool* pbool){{{1*/ void DoubleParam::GetParameterValue(bool* pbool){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - /*If debugging mode, cheeck that the double is 0 or 1*/ - _assert_(value==0 || value==1); - *pbool=(bool)value; - -#else _error_("Double param of enum %i (%s) cannot return an bool",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM){{{1*/ void DoubleParam::GetParameterValue(int** pintarray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - - output=(int*)xmalloc(1*sizeof(int)); - *output=(int)value; - - /*Assign output pointers:*/ - if(pM) *pM=1; - *pintarray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/ void DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - - output=(int*)xmalloc(1*sizeof(int)); - *output=(int)value; - - /*Assign output pointers:*/ - if(pM) *pM=1; - if(pN) *pN=1; - *pintarray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM){{{1*/ void DoubleParam::GetParameterValue(double** pdoublearray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - double* output=NULL; - - output=(double*)xmalloc(1*sizeof(double)); - *output=(double)value; - - /*Assign output podoubleers:*/ - if(pM) *pM=1; - *pdoublearray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){{{1*/ void DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - double* output=NULL; - - output=(double*)xmalloc(1*sizeof(double)); - *output=(double)value; - - /*Assign output podoubleers:*/ - if(pM) *pM=1; - if(pN) *pN=1; - *pdoublearray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type)); -#endif } -/*}}}*/ -/*FUNCTION DoubleParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar(value)); -} -#endif /*}}}*/ /*FUNCTION DoubleParam::UnitConversion{{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleTransientMatParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleTransientMatParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleTransientMatParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.cpp (revision 12168) @@ -75,61 +75,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleVecParam::Marshall{{{1*/ -void DoubleVecParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleVecParam: */ - enum_value=DoubleVecParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleVecParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleVecParam::MarshallSize{{{1*/ -int DoubleVecParam::MarshallSize(){ - - return sizeof(M) - +M*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleVecParam::Demarshall{{{1*/ -void DoubleVecParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - values=(double*)xmalloc(M*sizeof(double)); - memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleVecParam::ObjectEnum{{{1*/ int DoubleVecParam::ObjectEnum(void){ @@ -181,18 +124,5 @@ /*FUNCTION DoubleVecParam::GetParameterValue(int** pintarray,int* pM){{{1*/ void DoubleVecParam::GetParameterValue(int** pintarray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - int i; - - /*Cast values into integers*/ - output=(int*)xmalloc(M*sizeof(int)); - for(i=0;ienum_type); } -/*}}}*/ -/*FUNCTION DoubleVecParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleVecParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - double* doublevec=NULL; - mxArray* pfield=NULL; - - this->GetParameterValue(&doublevec,NULL); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, 0, name, pfield); -} -#endif /*}}}*/ /*FUNCTION DoubleVecParam::SetValue{{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.cpp (revision 12168) @@ -62,22 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION FileParam::Marshall{{{1*/ -void FileParam::Marshall(char** pmarshalled_dataset){ - - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -/*FUNCTION FileParam::MarshallSize{{{1*/ -int FileParam::MarshallSize(){ - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -/*FUNCTION FileParam::Demarshall{{{1*/ -void FileParam::Demarshall(char** pmarshalled_dataset){ - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -#endif /*FUNCTION FileParam::ObjectEnum{{{1*/ int FileParam::ObjectEnum(void){ @@ -101,12 +83,4 @@ } /*}}}*/ -/*FUNCTION FileParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void FileParam::SetMatlabField(mxArray* dataref){ - - _error_("FileParam is a pointer and cannot be converted into a matlab object"); -} -#endif -/*}}}*/ /*FUNCTION FileParam::UnitConversion{{{1*/ void FileParam::UnitConversion(int direction_enum){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -41,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -81,7 +72,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.cpp (revision 12168) @@ -78,64 +78,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntMatParam::Marshall{{{1*/ -void IntMatParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntMatParam: */ - enum_value=IntMatParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntMatParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,value,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntMatParam::MarshallSize{{{1*/ -int IntMatParam::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(int) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntMatParam::Demarshall{{{1*/ -void IntMatParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - value=(int*)xmalloc(M*N*sizeof(int)); - memcpy(value,marshalled_dataset,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntMatParam::ObjectEnum{{{1*/ int IntMatParam::ObjectEnum(void){ @@ -172,33 +112,4 @@ } /*}}}*/ -/*FUNCTION IntMatParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntMatParam::SetMatlabField(mxArray* dataref){ - - char *name = NULL; - double *doublearray = NULL; - int *intarray = NULL; - mxArray *pfield = NULL; - mxArray *pfield2 = NULL; - - this->GetParameterValue(&intarray,NULL,NULL); - this->GetParameterName(&name); - - /*cast intarray into doublearray for Matlab*/ - doublearray=(double*)xmalloc(M*N*sizeof(double)); - for(int i=0;i #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -83,7 +74,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.cpp (revision 12168) @@ -62,55 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntParam::Marshall{{{1*/ -void IntParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntParam: */ - enum_value=IntParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntParam::MarshallSize{{{1*/ -int IntParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntParam::Demarshall{{{1*/ -void IntParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntParam::ObjectEnum{{{1*/ int IntParam::ObjectEnum(void){ @@ -134,14 +83,4 @@ } /*}}}*/ -/*FUNCTION IntParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); -} -#endif -/*}}}*/ /*FUNCTION IntParam::UnitConversion{{{1*/ void IntParam::UnitConversion(int direction_enum){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.cpp (revision 12168) @@ -91,63 +91,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntVecParam::Marshall{{{1*/ -void IntVecParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntVecParam: */ - enum_value=IntVecParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntVecParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - if(M)memcpy(marshalled_dataset,values,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntVecParam::MarshallSize{{{1*/ -int IntVecParam::MarshallSize(){ - - return sizeof(M)+ - +M*sizeof(int) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntVecParam::Demarshall{{{1*/ -void IntVecParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M) { - values=(int*)xmalloc(M*sizeof(int)); - memcpy(values,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntVecParam::ObjectEnum{{{1*/ int IntVecParam::ObjectEnum(void){ @@ -185,33 +126,4 @@ } /*}}}*/ -/*FUNCTION IntVecParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntVecParam::SetMatlabField(mxArray* dataref){ - - char *name = NULL; - double *doublevec = NULL; - int *intvec = NULL; - mxArray *pfield = NULL; - - this->GetParameterValue(&intvec,NULL); - this->GetParameterName(&name); - - /*cast intvec into doublevec for Matlab*/ - if(M){ - doublevec=(double*)xmalloc(M*sizeof(double)); - for(int i=0;i #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -83,7 +74,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp (revision 12168) @@ -70,93 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION MatrixParam::Marshall{{{1*/ -void MatrixParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M,N; - double* serial_mat=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of MatrixParam: */ - enum_value=MatrixParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall MatrixParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - value->GetSize(&M,&N); - serial_mat=value->ToSerial(); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - } - else{ - M=0; - N=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - } - - /*Free ressources:*/ - xfree((void**)&serial_mat); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION MatrixParam::MarshallSize{{{1*/ -int MatrixParam::MarshallSize(){ - - int M=0; - int N=0; - if(value)value->GetSize(&M,&N); - - return sizeof(M)+ - sizeof(N)+ - M*N*sizeof(double)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION MatrixParam::Demarshall{{{1*/ -void MatrixParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int M,N; - double* serial_mat=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - if(M!=0 && N!=0){ - serial_mat=(double*)xmalloc(M*N*sizeof(double)); - memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - value=new Matrix(serial_mat,M,N,.001); - } - else{ - value=NULL; - } - - /*Free ressources:*/ - xfree((void**)&serial_mat); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION MatrixParam::ObjectEnum{{{1*/ int MatrixParam::ObjectEnum(void){ @@ -190,25 +101,4 @@ } /*}}}*/ -/*FUNCTION MatrixParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void MatrixParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - int M,N; - double* doublemat=NULL; - mxArray* pfield=NULL; - - doublemat=value->ToSerial(); - value->GetSize(&M,&N); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,N); - mxSetPr(pfield,doublemat); - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ /*FUNCTION MatrixParam::SetValue{{{1*/ void MatrixParam::SetValue(Matrix* matrix){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h (revision 12168) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -60,7 +56,4 @@ virtual void UnitConversion(int direction_enum)=0; virtual void GetParameterName(char**pname)=0; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - virtual void SetMatlabField(mxArray* dataref)=0; - #endif }; #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.cpp (revision 12168) @@ -92,96 +92,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringArrayParam::Marshall{{{1*/ -void StringArrayParam::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - char* string=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringArrayParam: */ - enum_value=StringArrayParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&numstrings,sizeof(numstrings));marshalled_dataset+=sizeof(numstrings); - for(i=0;ivalue[i]; - stringsize=strlen(string)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,string,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - } - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringArrayParam::MarshallSize{{{1*/ -int StringArrayParam::MarshallSize(){ - - int i; - int marshallsize=0; - int stringsize; - char* string=NULL; - - marshallsize+=sizeof(numstrings); - - for(i=0;ivalue[i]; - stringsize=strlen(string)+1; - marshallsize+=sizeof(stringsize); - marshallsize+=stringsize*sizeof(char); - } - - marshallsize+=sizeof(enum_type); - marshallsize+=sizeof(int); //sizeof(int) for enum value - - return marshallsize; -} -/*}}}*/ -/*FUNCTION StringArrayParam::Demarshall{{{1*/ -void StringArrayParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - char* string=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&numstrings,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(numstrings){ - this->value=(char**)xmalloc(numstrings*sizeof(char*)); - - for(i=0;ivalue[i]=string; - } - } - else this->value=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringArrayParam::ObjectEnum{{{1*/ int StringArrayParam::ObjectEnum(void){ @@ -236,26 +144,4 @@ } /*}}}*/ -/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringArrayParam::SetMatlabField(mxArray* dataref){ - - int i; - char* name=NULL; - mwSize dims[2]={0}; - mxArray* pfield=NULL; - - this->GetParameterName(&name); - - dims[0]=this->numstrings; - dims[1]=1; - pfield=mxCreateCellArray(2,dims); - for(i=0;inumstrings;i++){ - char* string=value[i]; - mxSetCell(pfield,i,mxCreateString(string)); - } - mxSetField( dataref, 0, name,pfield); -} -#endif -/*}}}*/ /*FUNCTION StringArrayParam::SetValue{{{1*/ void StringArrayParam::SetValue(char** stringarray,int M){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -44,9 +40,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.cpp (revision 12168) @@ -64,68 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringParam::Marshall{{{1*/ -void StringParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringParam: */ - enum_value=StringParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - stringsize=strlen(this->value)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringParam::MarshallSize{{{1*/ -int StringParam::MarshallSize(){ - - int stringsize; - stringsize=strlen(this->value)+1; - - return sizeof(int)+ - stringsize*sizeof(char)+ - sizeof(enum_type)+ - sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION StringParam::Demarshall{{{1*/ -void StringParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - - this->value=(char*)xmalloc(stringsize*sizeof(char)); - memcpy(this->value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringParam::ObjectEnum{{{1*/ int StringParam::ObjectEnum(void){ @@ -164,15 +100,4 @@ } /*}}}*/ -/*FUNCTION StringParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - - this->GetParameterName(&name); - mxSetField( dataref, 0, name, mxCreateString(value)); -} -#endif -/*}}}*/ /*FUNCTION StringParam::SetValue{{{1*/ void StringParam::SetValue(char* string){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp (revision 12168) @@ -72,88 +72,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION VectorParam::Marshall{{{1*/ -void VectorParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M; - double* serial_value=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of VectorParam: */ - enum_value=VectorParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall VectorParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - value->GetSize(&M); - serial_value=value->ToMPISerial(); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - } - else{ - M=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - } - /*Free ressources:*/ - xfree((void**)&serial_value); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION VectorParam::MarshallSize{{{1*/ -int VectorParam::MarshallSize(){ - - int M=0; - if(value)value->GetSize(&M); - - return sizeof(M)+M*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION VectorParam::Demarshall{{{1*/ -void VectorParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - double* serial_vec=NULL; - int M; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - serial_vec=(double*)xmalloc(M*sizeof(double)); - memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - - value=new Vector(serial_vec,M); - } - else{ - value=NULL; - } - - /*Free ressources:*/ - xfree((void**)&serial_vec); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION VectorParam::ObjectEnum{{{1*/ int VectorParam::ObjectEnum(void){ @@ -188,26 +104,4 @@ } /*}}}*/ -/*FUNCTION VectorParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void VectorParam::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - char* name=NULL; - double* doublevec=NULL; - int M; - - doublevec=value->ToMPISerial(); - value->GetSize(&M); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ /*FUNCTION VectorParam::SetValue{{{1*/ void VectorParam::SetValue(Vector* vector){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h (revision 12168) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Patch.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Patch.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Patch.cpp (revision 12168) @@ -120,13 +120,15 @@ int node_numrows; double *total_values = NULL; + #ifdef _HAVE_MPI_ MPI_Status status; + #endif - #ifdef _SERIAL_ - return; //nothing to be done - #endif - /*First, figure out total number of rows combining all the cpus: */ + #ifdef _HAVE_MPI_ MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD); + #else + total_numrows=this->numrows; + #endif /*return if patch empty*/ @@ -144,4 +146,5 @@ /*Now, ask other nodes to send their values: */ + #ifdef _HAVE_MPI_ for (i=1;inumcols. Update the fields in the patch, to reflect this new @@ -163,7 +167,9 @@ this->values=total_values; } + #ifdef _HAVE_MPI_ else{ this->numrows=0; xfree((void**)&this->values); } + #endif }/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Segment.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Segment.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Segment.cpp (revision 12168) @@ -71,22 +71,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Segment::Marshall{{{1*/ -void Segment::Marshall(char** pmarshalled_dataset){ - - _error_(" not supported yet!"); -} -/*}}}*/ -/*FUNCTION Segment::MarshallSize{{{1*/ -int Segment::MarshallSize(){ - _error_(" not supported yet!"); -} -/*}}}*/ -/*FUNCTION Segment::Demarshall{{{1*/ -void Segment::Demarshall(char** pmarshalled_dataset){ - _error_(" not supported yet!"); -} -/*}}}*/ -#endif /*FUNCTION Segment::ObjectEnum{{{1*/ int Segment::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Segment.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Segment.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Segment.h (revision 12168) @@ -30,9 +30,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp (revision 12168) @@ -92,78 +92,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Vertex::Marshall {{{1*/ -void Vertex::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Vertex: */ - enum_type=VertexEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Vertex data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&x,sizeof(x));marshalled_dataset+=sizeof(x); - memcpy(marshalled_dataset,&y,sizeof(y));marshalled_dataset+=sizeof(y); - memcpy(marshalled_dataset,&z,sizeof(z));marshalled_dataset+=sizeof(z); - memcpy(marshalled_dataset,&sigma,sizeof(sigma));marshalled_dataset+=sizeof(sigma); - memcpy(marshalled_dataset,&connectivity,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Vertex::MarshallSize {{{1*/ -int Vertex::MarshallSize(){ - - return sizeof(id)+ - sizeof(sid)+ - sizeof(x)+ - sizeof(y)+ - sizeof(z)+ - sizeof(sigma)+ - sizeof(connectivity)+ - sizeof(dof)+ - sizeof(clone)+ - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Vertex::Demarshall {{{1*/ -void Vertex::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&x,marshalled_dataset,sizeof(x));marshalled_dataset+=sizeof(x); - memcpy(&y,marshalled_dataset,sizeof(y));marshalled_dataset+=sizeof(y); - memcpy(&z,marshalled_dataset,sizeof(z));marshalled_dataset+=sizeof(z); - memcpy(&sigma,marshalled_dataset,sizeof(sigma));marshalled_dataset+=sizeof(sigma); - memcpy(&connectivity,marshalled_dataset,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Vertex::ObjectEnum{{{1*/ int Vertex::ObjectEnum(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h (revision 12168) @@ -47,9 +47,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/branches/trunk-jpl-damage/src/c/python/include/python_macros.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/include/python_macros.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/include/python_macros.h (revision 12168) @@ -0,0 +1,82 @@ +/* \file python_macros.h + * \brief: macros used for the python bindings + */ + +#ifndef _PYTHON_MACROS_H_ +#define _PYTHON_MACROS_H_ + +/*Header {{{1*/ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +/*}}}*/ + +#ifdef _HAVE_PYTHON_ +/* MODULEBOOT/MODULEEND {{{1*/ + +/*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +#define MODULEBOOT(); ModuleBoot(); \ + PyObject* output = PyTuple_New(NLHS); if (!output) return NULL;\ + int nrhs = (int)PyTuple_Size(args); + +#define MODULEEND(); ModuleEnd(); \ + return output; +//}}} +#if _PYTHON_MAJOR_ >=3 +/* WRAPPER 3.2 {{{1*/ +#define WRAPPER(modulename,...) \ +\ +static PyObject* modulename(PyObject* self,PyObject* args);\ +static PyMethodDef modulename##_funcs[] = {\ + {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ + {NULL,NULL,0,NULL}\ +};\ +\ +static struct PyModuleDef modulename##module= {\ + PyModuleDef_HEAD_INIT,\ + #modulename, /* name of module */\ + NULL, /* module documentation, may be NULL */\ + -1, /* size of per-interpreter state of the module,\ + or -1 if the module keeps state in global variables. */\ + modulename##_funcs\ +};\ +\ +PyMODINIT_FUNC PyInit_##modulename(void){\ +\ + import_array();\ + return PyModule_Create(&modulename##module);\ +}\ +\ +static PyObject* modulename(PyObject* self,PyObject* args) +/*}}}*/ +#else +/* WRAPPER 2.7 {{{1*/ +#define WRAPPER(modulename,...) \ +\ +static PyObject* modulename(PyObject* self,PyObject* args);\ +static PyMethodDef modulename##_funcs[] = {\ + {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ + {NULL,NULL,0,NULL}\ +};\ +\ +PyMODINIT_FUNC init##modulename(void){\ +\ + import_array();\ + (void) Py_InitModule(#modulename, modulename##_funcs);\ +}\ +\ +static PyObject* modulename(PyObject* self,PyObject* args) +/*}}}*/ +#endif +/* CHECKARGUMENTS {{{1*/ +#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) +/*}}}*/ +#endif + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/python/io/CheckNumPythonArguments.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/io/CheckNumPythonArguments.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/io/CheckNumPythonArguments.cpp (revision 12168) @@ -0,0 +1,36 @@ +/*!\file CheckNumPythonArguments.cpp: + * \brief: check number of arguments and report an usage error message. + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../shared/Exceptions/exceptions.h" +#include "../../include/include.h" + +int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){ + + Py_ssize_t size=0; + + /*figure out size of tuple in input: */ + size=PyTuple_Size(inputs); + + /*check on requested size: */ + if (size==0){ + function(); + _error_("usage: see above"); + } + else if (size!=NRHS ) { + function(); + _error_("usage error."); + } + return 1; +} Index: /issm/branches/trunk-jpl-damage/src/c/python/io/FetchPythonData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/io/FetchPythonData.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/io/FetchPythonData.cpp (revision 12168) @@ -0,0 +1,137 @@ +/*\file FetchData.cpp: + * \brief: general I/O interface to fetch data in python + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../include/include.h" +#include "../../shared/shared.h" + +/*Primitive data types*/ +/*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{1*/ +void FetchData(double* pscalar,PyObject* py_float){ + + double scalar; + + /*return internal value: */ + scalar=PyFloat_AsDouble(py_float); + + /*output: */ + *pscalar=scalar; +} +/*}}}*/ +/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{1*/ +void FetchData(int* pinteger, PyObject* py_long){ + + int integer; + + /*return internal value: */ + integer=(int)PyLong_AsLong(py_long); + + /*output: */ + *pinteger=integer; +} +/*}}}*/ +/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{1*/ +void FetchData(bool* pboolean,PyObject* py_boolean){ + + bool boolean; + + /*check this is indeed a subtype of long type: */ + if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!"); + + /*extract boolean: */ + boolean=(bool)PyLong_AsLong(py_boolean); + + /*simple copy: */ + *pboolean=boolean; + +} +/*}}}*/ +/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{1*/ +void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){ + + /*output: */ + double* matrix=NULL; + int M,N; + int ndim; + npy_intp* dims=NULL; + + /*retrive dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); + if(ndim!=2)_error_("expecting an MxN matrix in input!"); + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=dims[1]; + + /*retrieve internal value: */ + matrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); + + /*output: */ + if(pM)*pM=M; + if(pN)*pN=N; + if(pmatrix)*pmatrix=matrix; +} +/*}}}*/ +/*FUNCTION FetchData(double** pvector,int* pM, PyObject* py_vector){{{1*/ +void FetchData(double** pvector,int* pM,PyObject* py_vector){ + + /*output: */ + double* vector=NULL; + int M; + int ndim; + npy_intp* dims=NULL; + + /*retrive dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_vector); + if(ndim!=1)_error_("expecting an Mx1 vector in input!"); + dims=PyArray_DIMS((PyArrayObject*)py_vector); + M=dims[0]; + + /*retrieve internal value: */ + vector=(double*)PyArray_DATA((PyArrayObject*)py_vector); + + /*output: */ + if(pM)*pM=M; + if(pvector)*pvector=vector; +} +/*}}}*/ + +/*Python version dependent: */ +#if _PYTHON_MAJOR_ >= 3 +/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ +void FetchData(char** pstring,PyObject* py_unicode){ + + PyObject* py_bytes; + char* string=NULL; + + + /*convert to bytes format: */ + PyUnicode_FSConverter(py_unicode,&py_bytes); + + /*convert from bytes to string: */ + string=PyBytes_AS_STRING(py_bytes); + + *pstring=string; +} +/*}}}*/ +#else +/*FUNCTION FetchData(char** pstring,PyObject* py_string){{{1*/ +void FetchData(char** pstring,PyObject* py_string){ + + char* string=NULL; + + /*extract internal string: */ + string=PyString_AsString(py_string); + + *pstring=string; +} +/*}}}*/ +#endif Index: /issm/branches/trunk-jpl-damage/src/c/python/io/WritePythonData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/io/WritePythonData.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/io/WritePythonData.cpp (revision 12168) @@ -0,0 +1,78 @@ +/* \file WriteData.c: + * \brief: general interface for writing data + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../include/include.h" +#include "../../modules/modules.h" +#include "../../Container/Container.h" +#include "../../shared/shared.h" +#include "../../io/io.h" +#include "../../EnumDefinitions/EnumDefinitions.h" + + +/*FUNCTION WriteData(PyObject* py_tuple,int index,char* string){{{1*/ +void WriteData(PyObject* py_tuple, int index, char* string){ + + PyTuple_SetItem(py_tuple, index, PyUnicode_FromString(string)); + +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* tuple,int index,Matrix* matrix){{{1*/ +void WriteData(PyObject* tuple,int index,Matrix* matrix){ + + int M,N; + double* buffer=NULL; + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + buffer=matrix->ToSerial(); + matrix->GetSize(&M,&N); + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,buffer); + + PyTuple_SetItem(tuple, index, array); + + +} +/*FUNCTION WriteData(PyObject* py_tuple,int index,Vector* vector){{{1*/ +void WriteData(PyObject* tuple,int index,Vector* vector){ + + int M; + double* buffer=NULL; + npy_intp dim=10; + PyObject* array=NULL; + + buffer=vector->ToMPISerial(); + vector->GetSize(&M); + dim=(npy_intp)M; + array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer); + + PyTuple_SetItem(tuple, index, array); + + +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{1*/ +void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){ + + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix); + + PyTuple_SetItem(tuple, index, array); + +} Index: /issm/branches/trunk-jpl-damage/src/c/python/io/pythonio.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/io/pythonio.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/io/pythonio.h (revision 12168) @@ -0,0 +1,56 @@ +/*\file pythonio.h + *\brief: I/O for ISSM in python mode + */ + +#ifndef _PYTHON_IO_H_ +#define _PYTHON_IO_H_ + +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "../../objects/objects.h" +#include "../../Container/Container.h" +#include "../../include/include.h" + +class DataSet; +class Parameters; + +//void WriteData(PyObject* py_tuple,DataSet* dataset); +//void WriteData(PyObject* py_tuple,int* matrix, int M,int N); +//void WriteData(PyObject* py_tuple,double* vector, int M); +//void WriteData(PyObject* py_tuple,int integer); +//void WriteData(PyObject* py_tuple,bool boolean); +//void WriteData(PyObject* py_tuple,double scalar); +//void WriteData(DataHandle* py_tuple,Parameters* parameters); +void WriteData(PyObject* py_tuple, int index, double* matrix, int M,int N); +void WriteData(PyObject* py_tuple, int index, char* string); +void WriteData(PyObject* py_tuple, int index, Matrix* matrix); +void WriteData(PyObject* py_tuple, int index, Vector* vector); + + +//void FetchData(DataSet** pdataset,PyObject* py_ref); +//void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_ref); +//void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_ref); +//void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(Matrix** pmatrix,PyObject* py_ref); +//void FetchData(int** pvector,int* pM,PyObject* py_ref); +//void FetchData(float** pvector,int* pM,PyObject* py_ref); +//void FetchData(bool** pvector,int* pM,PyObject* py_ref); +//void FetchData(Vector** pvector,PyObject* py_ref); +//void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(Parameters** pparameters, DataHandle py_ref); +void FetchData(double** pvector,int* pM,PyObject* py_ref); +void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array); +void FetchData(char** pstring,PyObject* py_unicode); +void FetchData(double* pscalar,PyObject* py_float); +void FetchData(int* pinteger,PyObject* py_long); +void FetchData(bool* pbool,PyObject* py_boolean); + +int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )); + +#endif /* _IO_H_ */ Index: /issm/branches/trunk-jpl-damage/src/c/python/python-binding.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/python/python-binding.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/python/python-binding.h (revision 12168) @@ -0,0 +1,7 @@ +#ifndef _PYTHON_BINDING_H_ +#define _PYTHON_BINDING_H_ + +#include "./io/pythonio.h" +#include "./include/python_macros.h" + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 12168) @@ -19,8 +19,4 @@ #endif -#if defined(_SERIAL_) && defined(_HAVE_MATLAB_) -#include "mex.h" -#endif - #include #include @@ -37,11 +33,6 @@ if(!size)_error_(" attempting to 0 size allocation!"); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - /* Use the matlab api to do the allocation: */ - memptr=mxMalloc(size); - #else /* Use the c library to do the allocation: */ memptr=malloc(size); - #endif if(!memptr) _error_("memory allocation failed!"); @@ -55,11 +46,6 @@ if(!size)_error_("attempting to 0 size allocation!"); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - /* Use the matlab api to do the allocation: */ - memptr=mxCalloc(n,size); - #else /* Use the c library to do the allocation: */ memptr=calloc(n,size); - #endif if(!memptr) _error_("memory allocation failed!"); @@ -70,9 +56,5 @@ if (pv && *pv){ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxFree(*pv); - #else - free(*pv); - #endif + free(*pv); *pv=NULL; @@ -83,16 +65,8 @@ if (pv && *pv){ - #ifdef _PARALLEL_ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we * don't actually free memory in Matlab, we let the memory manager do that. We only * free in parallel: */ delete *pv; - #else - /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ - * correctly: */ - #ifdef _HAVE_PETSC_ - MatFree(&(*pv)->matrix); - #endif - #endif *pv=NULL; } @@ -102,16 +76,8 @@ if (pv && *pv){ - #ifdef _PARALLEL_ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we * don't actually free memory in Matlab, we let the memory manager do that. We only * free in parallel: */ delete *pv; - #else - /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ - * correctly: */ - #ifdef _HAVE_PETSC_ - VecFree(&(*pv)->vector); - #endif - #endif *pv=NULL; } @@ -124,10 +90,5 @@ if(!size)_error_("attempting to realloc to zero"); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - value = (void*)mxRealloc(pv,size); - #else value = (void*)realloc(pv,size); - #endif if (value == NULL) { Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.cpp (revision 12168) @@ -0,0 +1,41 @@ +/* \file alloc_module.h + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include + +#include "./alloc_module.h" +#include "../Exceptions/exceptions.h" +#include "../../include/include.h" +#include "../../objects/objects.h" + +void xdelete_module(Matrix** pv){ + + if (pv && *pv){ + /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ + * correctly: */ + #ifdef _HAVE_PETSC_ + MatFree(&(*pv)->matrix); + #endif + *pv=NULL; + } +} + +void xdelete_module(Vector** pv){ + + if (pv && *pv){ + /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ + * correctly: */ + #ifdef _HAVE_PETSC_ + VecFree(&(*pv)->vector); + #endif + *pv=NULL; + } +} Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc_module.h (revision 12168) @@ -0,0 +1,11 @@ +/* \file alloc.h + */ + +#ifndef _ALLOC_MODULE_H_ +#define _ALLOC_MODULE_H_ +class Matrix; +class Vector; +void xdelete_module(Matrix** pvptr); +void xdelete_module(Vector** pvptr); + +#endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/Exceptions.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/Exceptions.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/Exceptions.cpp (revision 12168) @@ -11,7 +11,4 @@ #include "../shared.h" #include "../../include/include.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif ErrorException::ErrorException(const string &what_arg){ @@ -32,4 +29,8 @@ ErrorException::~ErrorException() throw(){ + extern int num_procs; + /*We want the report only for matlab modules, otherwise we get twice the report + * We assume that if num_procs==1, it is a module (FIXME)*/ + if(num_procs==1) this->Report(); } @@ -40,4 +41,5 @@ void ErrorException::Report(){ extern int my_rank; + extern int num_procs; if (function_name=="" || file_line==0){ //WINDOWS @@ -45,11 +47,12 @@ } else{ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mexErrMsgTxt(exprintf("\n??? Error using ==> %s at %i\n%s error message: %s\n", - file_name.c_str(),file_line,function_name.c_str(),what())); - #else + if(num_procs==1){ + printf("\n??? Error using ==> %s:%i\n",file_name.c_str(),file_line); + printf("%s error message: %s\n\n",function_name.c_str(),what()); + } + else{ printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); - #endif + } } return; Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/exceptions.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/exceptions.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exceptions/exceptions.h (revision 12168) @@ -23,11 +23,8 @@ public: - ErrorException(const string &what_arg); //for windows ErrorException(string what_file,string what_function,int what_line,string what_arg);//UNIX ~ErrorException() throw(); - virtual const char *what() const throw(); - void Report(); Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineRead.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12168) @@ -13,6 +13,5 @@ #include "../../Container/DataSet.h" -int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole=true){ - +int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname){ /*indexing: */ @@ -102,7 +101,4 @@ if((x[0]==x[n-1]) && (y[0]==y[n-1])){ cl=true; - if (!whole) { - n=n-1; - } } @@ -126,30 +122,30 @@ } -DataSet* DomainOutlineRead(char* domainname,bool whole=true){ - - /*indexing: */ - int i; +DataSet* DomainOutlineRead(char* domainname){ /*intermediary: */ - int nprof; - int* profnvertices=NULL; - double** pprofx=NULL; - double** pprofy=NULL; - - Contour* contour=NULL; + int nprof; + int *profnvertices = NULL; + double **pprofx = NULL; + double **pprofy = NULL; + Contour *contour = NULL; /*output: */ DataSet* domain=NULL; - /*get domain outline from intermediary function:*/ - DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname,whole); + /*If domainname is an empty string, return empty dataset*/ + if (strcmp(domainname,"")==0){ + nprof=0; + } + else{ + DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname); + } /*now create dataset of contours: */ domain=new DataSet(0); - for(i=0;iAddObject(new Contour(i,profnvertices[i],pprofx[i],pprofy[i],1)); } - return domain; } Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineWrite.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12168) @@ -11,5 +11,5 @@ #include "../Exceptions/exceptions.h" -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole=true){ +int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname){ @@ -20,11 +20,4 @@ /*I/O: */ FILE* fid=NULL; - - /*input: */ -// int nprof; //number of profiles in the domainname file -// int* profnvertices=NULL; //array holding the number of vertices for the nprof profiles -// double** pprofx=NULL; //array of profiles x coordinates -// double** pprofy=NULL; //array of profiles y coordinates -// bool* closed=NULL; //array holding closed flags for the nprof profiles /*open domain outline file for writing: */ @@ -43,8 +36,5 @@ /*Write number of profile vertices: */ - if(closed[counter] && !whole) - fprintf(fid,"%u %s\n",profnvertices[counter]+1,"1."); - else - fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); + fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); /*Write next line: */ @@ -55,8 +45,4 @@ fprintf(fid,"%lf\t%lf\n",pprofx[counter][i],pprofy[counter][i]); } - - /*Now check that we are dealing with open contours: */ - if(closed[counter] && !whole) - fprintf(fid,"%lf\t%lf\n",pprofx[counter][0],pprofy[counter][0]); /*Write blank line: */ Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h (revision 12168) @@ -13,9 +13,9 @@ int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue); -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole); +int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname); int pnpoly(int npol, double *xp, double *yp, double x, double y, int edgevalue); -int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole); -DataSet* DomainOutlineRead(char* domainname,bool whole); +int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname); +DataSet* DomainOutlineRead(char* domainname); Index: sm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptFunc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptFunc.cpp (revision 12167) +++ (revision ) @@ -1,41 +1,0 @@ -/*!\file: OptFunc.cpp - * \brief: "C" code wrapper to matlab objectivefunctionC call - */ - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include "../../objects/objects.h" -#include "../../shared/shared.h" -#include "../../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -double OptFunc(double scalar, OptArgs* optargs){ - - /*output: */ - double J; - - mxArray* inputs[2]; - mxArray* psearch_scalar=NULL; - mxArray* mxJ=NULL; - - psearch_scalar=mxCreateDoubleScalar(scalar); - inputs[0]=psearch_scalar; - inputs[1]=optargs->femmodel; - - mexCallMATLAB(1,&mxJ,2,(mxArray**)inputs, optargs->function_name); - - /*extract misfit from mxArray*/ - J=mxGetScalar(mxJ); - - return J; -} -#else -double OptFunc(double scalar, OptArgs* optargs){ - _error_(" not implemented yet"); -} -#endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12168) @@ -30,11 +30,5 @@ parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis - if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); - } - else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #endif if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. Index: /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Synchronize.sh =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Synchronize.sh (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Synchronize.sh (revision 12168) @@ -2,5 +2,5 @@ #Synchronize Verbosity #first remove existing files -rm $ISSM_TIER/src/m/shared/Verb*.m +rm $ISSM_DIR/src/m/shared/Verb*.m echo "Synchronizing Verbosity levels..." @@ -29,7 +29,4 @@ #include "../../include/macros.h" #include "../Exceptions/exceptions.h" -#ifdef _SERIAL_ -#include -#endif /*}}}*/ @@ -54,5 +51,5 @@ #Add Verbosity Matlab file{{{ - cat < $ISSM_TIER"/src/m/shared/"$(echo $FILENAME".m") + cat < $ISSM_DIR"/src/m/shared/"$(echo $FILENAME".m") function bool=$(echo $FILENAME)() %$(echo $FILENAME | awk {'print toupper($1)'}) - Return true if $(echo $LEVELNAME | awk {'print tolower($1)'}) level is activated @@ -140,42 +137,16 @@ if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); -#ifdef _SERIAL_ - - mxArray* output=NULL; - mxArray* input=NULL; - input=mxCreateDoubleScalar((double)level); - - mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); -#else - verbositylevel = level; -#endif }/*}}}*/ /*FUNCTION GetVerbosityLevel {{{*/ int GetVerbosityLevel(void){ -#ifdef _SERIAL_ - - mxArray* output=NULL; - mxArray* input=NULL; - double level; - - mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); - level=mxGetScalar(output); - - verbositylevel = (int)level; - return verbositylevel; - -#else - _assert_(verbositylevel>=0); return verbositylevel; - -#endif }/*}}}*/ END #}}} #Complete verbose.m {{{1 -VERBOSEPATH="$ISSM_TIER/src/m/classes/verbose.m" +VERBOSEPATH="$ISSM_DIR/src/m/classes/verbose.m" cat $VERBOSEPATH | sed "/%BEGINFIELDS/,$ d" > temp_begin cat $VERBOSEPATH | sed "1,/%ENDFIELDS/d" > temp_end Index: /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Verbosity.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Verbosity.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/Verbosity.cpp (revision 12168) @@ -18,7 +18,4 @@ #include "../../include/macros.h" #include "../Exceptions/exceptions.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif /*}}}*/ @@ -39,36 +36,12 @@ if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - mxArray* output=NULL; - mxArray* input=NULL; - input=mxCreateDoubleScalar((double)level); - - mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); -#else - verbositylevel = level; -#endif }/*}}}*/ /*FUNCTION GetVerbosityLevel {{{*/ int GetVerbosityLevel(void){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - mxArray* output=NULL; - mxArray* input=NULL; - double level; - - mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); - level=mxGetScalar(output); - - verbositylevel = (int)level; - return verbositylevel; - -#else _assert_(verbositylevel>=0); return verbositylevel; -#endif }/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12168) @@ -1,6 +1,6 @@ -#include "../../io/Matlab/matlabio.h" #include "../Alloc/alloc.h" #include "../../include/include.h" #include "../Exceptions/exceptions.h" +#include "./isnan.h" #include Index: /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/SplitMeshForRifts.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12168) @@ -47,8 +47,7 @@ segmentmarkerlist=*psegmentmarkerlist; - /*Establish list of segments that belong to a rift: */ - RiftSegmentsFromSegments(&nriftsegs,&riftsegments,nel,index,nsegs,segments); /*riftsegments of size nriftsegsx4 (4 for first element on segment,second element, - first node and second snode)*/ + /*riftsegments of size nriftsegsx4 (4 for first element on segment,second element,first node and second snode)*/ + RiftSegmentsFromSegments(&nriftsegs,&riftsegments,nel,index,nsegs,segments); /*Go through all nodes of the rift segments, and start splitting the mesh: */ @@ -57,5 +56,5 @@ for (j=0;j<2;j++){ - node=*(riftsegments+4*i+j+2); + node=riftsegments[4*i+j+2]; if(flags[node-1]){ /*This node was already split, skip:*/ @@ -70,7 +69,11 @@ DetermineGridElementListOnOneSideOfRift(&NumGridElementListOnOneSideOfRift,&GridElementListOnOneSideOfRift,i,nriftsegs,riftsegments,node,index,nel); - /*Summary: we have for node, a list of elements (GridElementListOnOneSideOfRift, of size NumGridElementListOnOneSideOfRift) that all contain node - *and that are on the same side of the rift. For all these elements, we clone node into another node, and we swap all instances of node in the triangulation - *for those elements, to the new node.*/ + /*Summary: we have for node, a list of elements + * (GridElementListOnOneSideOfRift, of size + * NumGridElementListOnOneSideOfRift) that all contain node + *and that are on the same side of the rift. For all these + elements, we clone node into another node, and we swap all + instances of node in the triangulation *for those elements, to the + new node.*/ //augment number of nodes @@ -94,5 +97,5 @@ /*update segments: they got modified completely by adding new nodes.*/ - UpdateSegments(&segments,&segmentmarkerlist, &nsegs,index,x,y,riftsegments,nriftsegs); + UpdateSegments(&segments,&segmentmarkerlist, &nsegs,index,x,y,riftsegments,nriftsegs,nods,nel); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/TriMeshUtils.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/TriMeshUtils.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/TriMeshUtils.cpp (revision 12168) @@ -11,4 +11,5 @@ #define RIFTPENALTYPAIRSWIDTH 8 +/*FUNCTION IsGridOnRift{{{*/ int IsGridOnRift(int* riftsegments, int nriftsegs, int node){ @@ -32,7 +33,6 @@ return 0; } -} - - +}/*}}}*/ +/*FUNCTION GridElementsList{{{*/ int GridElementsList(int** pGridElements, int* pNumGridElements,int node,double * index,int nel){ @@ -87,7 +87,6 @@ *pNumGridElements=NumGridElements; return noerr; -} - - +}/*}}}*/ +/*FUNCTION IsNeighbor{{{*/ int IsNeighbor(int el1,int el2,double* index){ /*From a triangulation held in index, figure out if elements 1 and 2 have two nodes in common: */ @@ -105,7 +104,6 @@ return 0; } -} - - +}/*}}}*/ +/*FUNCTION IsOnRift{{{*/ int IsOnRift(int el,int nriftsegs,int* riftsegments){ /*From a list of elements segments, figure out if el belongs to it: */ @@ -117,11 +115,6 @@ } return 0; -} - - -/****************************************************************************************************************************** - RiftSegmentsFromSegments -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION RiftSegmentsFromSegments{{{*/ void RiftSegmentsFromSegments(int* pnriftsegs, int** priftsegments, int nel, double* index, int nsegs,double* segments){ @@ -189,10 +182,6 @@ *priftsegments=riftsegments; *pnriftsegs=nriftsegs; -} - -/****************************************************************************************************************************** - DetermineGridElementListOnOneSideOfRift -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION DetermineGridElementListOnOneSideOfRift{{{*/ int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel){ @@ -257,11 +246,7 @@ *pGridElementListOnOneSideOfRift=GridElementListOnOneSideOfRift; return noerr; -} - -/****************************************************************************************************************************** - UpdateSegments -******************************************************************************************************************************/ - -int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs){ +}/*}}}*/ +/*FUNCTION UpdateSegments{{{*/ +int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel){ int noerr=1; @@ -284,8 +269,8 @@ /*First, update the existing segments to the new nodes :*/ for (i=0;i0 && node4>0); + if ((x[node1-1]==x[node4-1]) && (y[node1-1]==y[node4-1])){ /*Swap node3 and node4:*/ temp_node=node3; @@ -943,10 +874,6 @@ *priftstips=riftstips; return noerr; -} - -/****************************************************************************************************************************** - PenaltyPairs -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION PenaltyPairs{{{*/ int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, int* riftsnumsegs,double** riftspairs,double* riftstips,double* x,double* y){ Index: /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/trimesh.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/trimesh.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/TriMesh/trimesh.h (revision 12168) @@ -6,20 +6,13 @@ #define _SHARED_TRIMESH_H - #include #include - - //#define REAL double //took it out because it may conflict with stdlib.h defines. put back if necessary - int AssociateSegmentToElement(double** psegments,int nseg, double* index,int nel); int OrderSegments(double** psegments,int nseg, double* index,int nel); - int GridInsideHole(double* px0,double* py0,int n,double* x,double* y); int FindElement(double A,double B,double* index,int nel); - int SplitMeshForRifts(int* pnel,double** pindex,int* pnods,double** px,double** py,int* pnsegs,double** psegments,double** psegmentmarkerlist); - int IsGridOnRift(int* riftsegments, int nriftsegs, int node); int GridElementsList(int** pGridElements, int* pNumGridElements,int node,double * index,int nel); @@ -28,17 +21,15 @@ void RiftSegmentsFromSegments(int* pnriftsegs, int** priftsegments, int nel, double* index, int nsegs,double* segments); int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel); -int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs); +int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel); int pnpoly(int npol, double *xp, double *yp, double x, double y); int FindElement(double A,double B,double* index,int nel); int RemoveRifts(double** pindex,double** px,double** py,int* pnods,double** psegments,int* pnumsegs,int numrifts1,int* rifts1numsegs,double** rifts1segments,double** rifts1pairs,int nel); int IsRiftPresent(int* priftflag,int* pnumrifts, double* segmentmarkerlist,int nsegs); -int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts); -int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y); +int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts,int nods,int nels); +int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y,int nods,int nels); int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, int* riftsnumsegments,double** riftspairs,double* riftstips,double* x,double* y); - int RemoveCornersFromRifts(double** pindex,int* pnel,double** px,double** py,int* pnods, double* segments,double* segmentmarkers,int num_seg); int PairRiftElements(int** priftsnumpairs, double*** priftspairs,int numrifts,int* riftsnumsegments, double** riftssegments,double* x,double* y); - #endif /* _SHARED_TRIMESH_H */ Index: /issm/branches/trunk-jpl-damage/src/c/shared/Wrapper/wrappershared.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Wrapper/wrappershared.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Wrapper/wrappershared.h (revision 12168) @@ -8,8 +8,6 @@ #include "../../objects/objects.h" -#ifdef _SERIAL_ int ModuleBoot(void); int ModuleEnd(void); -#endif #endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/shared.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/shared.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/shared/shared.h (revision 12168) @@ -8,4 +8,5 @@ #include "Alloc/alloc.h" +#include "Alloc/alloc_module.h" #include "Exceptions/exceptions.h" #include "Exp/exp.h" Index: /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp (revision 12168) @@ -35,9 +35,5 @@ int ierr; - MODULEBOOT(); - - #ifndef _PARALLEL_ - _error_(" parallel executable was compiled without support of parallel libraries!"); - #endif + ISSMBOOT(); /*Initialize environments: Petsc, MPI, etc...: */ @@ -46,12 +42,20 @@ if(ierr) _error_("Could not initialize Petsc"); #else + #ifdef _HAVE_MPI_ MPI_Init(&argc,&argv); #endif + #endif + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); + #else + start=(double)clock(); + #endif /*Size and rank: */ + #ifdef _HAVE_MPI_ MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); MPI_Comm_size(MPI_COMM_WORLD,&num_procs); + #endif /*First process inputs*/ @@ -66,5 +70,9 @@ /*Create femmodel, using input file: */ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); + #else + start_init=(double)clock(); + #endif femmodel=new FemModel(binfilename,outbinfilename,solution_type,analyses,numanalyses); @@ -86,8 +94,17 @@ femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime(); + #else + finish_init=(double)clock(); + #endif _printf_(true,"call computational core:\n"); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( ); + #else + start_core=(double)clock(); + #endif + if(dakota_analysis){ #ifdef _HAVE_DAKOTA_ @@ -110,6 +127,10 @@ solutioncore(femmodel); } + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( ); - + #else + finish_core=(double)clock(); + #endif + _printf_(true,"write results to disk:\n"); OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); @@ -131,21 +152,31 @@ /*Get finish time and close*/ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish = MPI_Wtime( ); _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",finish_init-start_init); _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); + #else + finish=(double)clock(); + _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",(finish_init-start_init)/CLOCKS_PER_SEC); + _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",(finish_core-start_core)/CLOCKS_PER_SEC); + _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600/CLOCKS_PER_SEC),int(int((finish-start)/CLOCKS_PER_SEC)%3600/60),(int(finish-start)/CLOCKS_PER_SEC)%60); + #endif + + #ifdef _HAVE_PETSC_ _printf_(true,"closing MPI and Petsc\n"); - #ifdef _HAVE_PETSC_ PetscFinalize(); #else + #ifdef _HAVE_MPI_ + _printf_(true,"closing MPI and Petsc\n"); MPI_Finalize(); + #endif #endif /*end module: */ - MODULEEND(); + ISSMEND(); return 0; //unix success return; } - Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.cpp (revision 12168) @@ -92,52 +92,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION SeqMat::ToMatlabMatrix{{{1*/ -mxArray* SeqMat::ToMatlabMatrix(void){ - - /*Intermediary: */ - double* buffer=NULL; - mxArray* pfield=NULL; - - /*output: */ - mxArray* dataref=NULL; - - /*copy vector into a new buffer: */ - if(this->M*this->N){ - buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); - memcpy(buffer,this->matrix,M*N*sizeof(double)); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,this->N); - mxSetN(pfield,this->M); - mxSetPr(pfield,buffer); - - //transpose the matrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&dataref, 1, &pfield, "transpose"); - } - else dataref=mxCreateDoubleMatrix(0,0,mxREAL); - - /*do not erase buffer!: */ - return dataref; - -} - - - - -/*}}}*/ -/*FUNCTION MatlabMatrixToSeqMat{{{1*/ -SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ - - SeqMat* output=NULL; - - output=new SeqMat(); - MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); - return output; - -} -/*}}}*/ -#endif /*FUNCTION SeqMat::Assemble{{{1*/ void SeqMat::Assemble(void){ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqMat.h (revision 12168) @@ -15,8 +15,4 @@ #include "../toolkitsenums.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif /*}}}*/ @@ -40,7 +36,4 @@ /*SeqMat specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabMatrix(void); - #endif void Assemble(void); double Norm(NormMode norm_type); @@ -56,8 +49,3 @@ }; -/*API :*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); -#endif - #endif //#ifndef _SEQMAT_H_ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.cpp (revision 12168) @@ -66,42 +66,4 @@ /*}}}*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION SeqVec::ToMatlabVector{{{1*/ -mxArray* SeqVec::ToMatlabVector(void){ - - double* buffer=NULL; - - mxArray* dataref=NULL; - - /*copy vector into a new buffer: */ - if(this->M){ - buffer=(double*)xmalloc(this->M*sizeof(double)); - memcpy(buffer,vector,M*sizeof(double)); - - dataref = mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(dataref,this->M); - mxSetN(dataref,1); - mxSetPr(dataref,buffer); - } - else dataref = mxCreateDoubleMatrix(0,0,mxREAL); - - - /*do not erase buffer!: */ - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabVectorToSeqVec{{{1*/ -SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ - - SeqVec* output=NULL; - - output=new SeqVec(); - MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); - return output; - -} -/*}}}*/ -#endif /*FUNCTION SeqVec::Assemble{{{1*/ void SeqVec::Assemble(void){ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/issm/SeqVec.h (revision 12168) @@ -15,8 +15,4 @@ #include "../toolkitsenums.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif /*}}}*/ @@ -37,7 +33,4 @@ /*SeqVec specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabVector(void); - #endif void Assemble(void); void SetValues(int ssize, int* list, double* values, InsMode mode); @@ -59,9 +52,3 @@ }; - -/*API :*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); -#endif - #endif //#ifndef _SEQVEC_H_ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatInvert.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12168) @@ -55,10 +55,6 @@ MatAssemblyBegin(inv,MAT_FINAL_ASSEMBLY); MatAssemblyEnd(inv,MAT_FINAL_ASSEMBLY); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - MatConvert(inv, MATSEQAIJ,MAT_REUSE_MATRIX,&inv); - #else - MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); - #endif + + MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); /*Free ressources:*/ Index: sm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 12167) +++ (revision ) @@ -1,123 +1,0 @@ -/* \file MatlabMatrixToPetscMatrix.cpp - * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix: - */ - - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ - - int rows, cols; - double* mxmatrix_ptr=NULL; - double* tmatrix=NULL; - int ierr; - int i,j; - - /*output: */ - Mat matrix=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; - - /*petsc indices: */ - int* idxm=NULL; - int* idxn=NULL; - - /*Ok, first check if we are dealing with a sparse or full matrix: */ - if (mxIsSparse(mxmatrix)){ - - /*Dealing with sparse matrix: recover size first: */ - mxmatrix_ptr=(double*)mxGetPr(mxmatrix); - rows=mxGetM(mxmatrix); - cols=mxGetN(mxmatrix); - nnz=mxGetNzmax(mxmatrix); - if(rows){ - nz=(int)((double)nnz/(double)rows); - } - else{ - nz=0; - } - - ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr); - - /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxmatrix); - ir=mxGetIr(mxmatrix); - jc=mxGetJc(mxmatrix); - - /*Now, start inserting data into sparse matrix: */ - count=0; - for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ - - int rows, cols; - double* mxvector_ptr=NULL; - int ierr; - int i,j; - - /*output: */ - Vec vector=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; - - /*petsc indices: */ - int* idxm=NULL; - - /*Ok, first check if we are dealing with a sparse or full vector: */ - if (mxIsSparse(mxvector)){ - - /*Dealing with sparse vector: recover size first: */ - mxvector_ptr=(double*)mxGetPr(mxvector); - rows=mxGetM(mxvector); - cols=mxGetN(mxvector); - nnz=mxGetNzmax(mxvector); - nz=(int)((double)nnz/(double)rows); - - ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr); - - /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxvector); - ir=mxGetIr(mxvector); - jc=mxGetJc(mxvector); - - /*Now, start inserting data into sparse vector: */ - count=0; - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Petsc includes: */ +#include "../../../shared/shared.h" + + +void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ + + int i,j,k; + + /*output: */ + double* matrix=NULL; + int rows,cols; + + /*intermediary: */ + int* idxm=NULL; + int* idxn=NULL; + + /*Some needed information: */ + MatGetSize(petsc_matrix,&rows,&cols); + + idxm=(int*)xmalloc(rows*sizeof(int)); + idxn=(int*)xmalloc(cols*sizeof(int)); + + for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Petsc includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" -#include - - -int PetscMatrixToMatlabMatrix(mxArray** pdataref,Mat tmatrix){ - - int i,j,k; - - /*output: */ - mxArray* dataref=NULL; - int rows,cols; - - int ncols; - int nnz=0; - int nzmax=0; - const int* columns=NULL; - const double* column_values=NULL; - double* matrix_ptr=NULL; - - /*compress row format: */ - double* val=NULL; - mwIndex* col_ind=NULL; - mwIndex* row_ptr=NULL; - - /*petsc type: */ - const char* type=NULL; - int* idxm=NULL; - int* idxn=NULL; - Mat matrix=NULL; - - - /*First off, we need to transpose the matrix using the Petsc API. We tried using the transpose operation from - * Matlab, but this ends up creating issues with lost pointers and references: */ - MatTranspose(tmatrix,MAT_INITIAL_MATRIX,&matrix); - - /*Some needed information: */ - MatGetType(matrix,&type); - MatGetSize(matrix,&rows,&cols); - - if (strcmp(type,MATSEQAIJ)==0){ - - /*Dealing with a sparse sequential matrix: build ir, jc and val, as though it was a row comvalessed - *format, instead of a column comvalessed format. We'll transpose later.*/ - - /*First get nnz: */ - nnz=0; - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +#include "../../../shared/shared.h" + +void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ + + int i; + int rows; + int *idxm = NULL; + double *vector = NULL; + + /*Get size of vector: */ + if(petsc_vector){ + VecGetSize(petsc_vector,&rows); + if(rows){ + idxm=(int*)xmalloc(rows*sizeof(int)); + vector=(double*)xmalloc(rows*sizeof(double)); + for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Petsc includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" -#include - - -int PetscVectorToMatlabVector(mxArray** pdataref,Vec vector){ - - int i; - int rows; - int *idxm = NULL; - double *values = NULL; - - /*output: */ - mxArray* dataref=NULL; - - /*Get size of vector: */ - if(vector){ - VecGetSize(vector,&rows); - if(rows){ - idxm=(int*)xmalloc(rows*sizeof(int)); - values=(double*)xmalloc(rows*sizeof(double)); - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#if _PYTHON_MAJOR_ == 2 +#undef NPY_NO_DEPRECATED_API +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION +#else +#define NPY_NO_DEPRECATED_API +#endif + #include "Python.h" #include "arrayobject.h" - - #ifdef _HAVE_BOOST_ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h (revision 12168) @@ -12,5 +12,5 @@ #endif -#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) +#ifdef _HAVE_PYTHON_ #include "./python/pythonincludes.h" #endif @@ -20,13 +20,13 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "./matlab/matlabincludes.h" +#ifdef _HAVE_MPI_ +#include "./mpi/mpiincludes.h" #endif +#ifdef _HAVE_METIS_ +#include "./metis/metisincludes.h" +#endif -#include "./mpi/mpiincludes.h" -#include "./metis/metisincludes.h" #include "./triangle/triangleincludes.h" -#include "./double/double.h" #include "./toolkitsenums.h" #include "./issm/issmtoolkit.h" Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/triangle/triangleincludes.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/triangle/triangleincludes.h (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/triangle/triangleincludes.h (revision 12168) @@ -6,6 +6,4 @@ #define _TRIANGLE_INCLUDES_H_ -#ifdef _SERIAL_ - #ifdef _C_ //only valid for iso C, not C++ /*Triangle includes: */ @@ -13,6 +11,4 @@ #endif //#ifdef _C_ -#endif //ifdef _SERIAL_ - #endif Index: /issm/branches/trunk-jpl-damage/src/dox/issm.dox =================================================================== --- /issm/branches/trunk-jpl-damage/src/dox/issm.dox (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/dox/issm.dox (revision 12168) @@ -46,20 +46,20 @@ - + - + - + - + - + - + @@ -67,14 +67,14 @@ - + - + - + - +
C++ 53315491172755800590771 C++ 49914338163405465185329
MATLAB 9777199137023169052591 MATLAB 9196875131843035050409
C/C++ Header 399306927271035816154 C/C++ Header 36626652529940014594
m4 71061242894110244 m4 79938082379310
Objective C 9980370468 Python 4718351810991800
Bourne Shell 86198271430 Objective C 9980370468
IDL 1184124146 Bourne Shell 54671226343
C 2332430 IDL 1184124146
Python 2141318 C 2332430
SUM: 19412702234078110036171136 SUM: 18582524032752104721162713
Index: /issm/branches/trunk-jpl-damage/src/m/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/Makefile.am (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/Makefile.am (revision 12168) @@ -13,9 +13,5 @@ ./planet/*.m \ ./qmu/*.m \ - ./shared/*.m \ - ./solutions/*.m \ - ./solvers/*.m \ ./utils/*.m \ - ./utils/Analysis/*.m \ ./utils/Array/*.m \ ./utils/BC/*.m \ Index: /issm/branches/trunk-jpl-damage/src/m/classes/autodiff.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/autodiff.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/autodiff.py (revision 12168) @@ -0,0 +1,28 @@ +#module imports +from fielddisplay import fielddisplay + +class autodiff: + #properties + def __init__(self): + # {{{ Properties + self.isautodiff = False + self.forward = True + self.reverse = False + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' automatic differentiation parameters:' + string="%s\n%s"%(string,fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated')) + string="%s\n%s"%(string,fielddisplay(obj,'forward','forward differentiation')) + string="%s\n%s"%(string,fielddisplay(obj,'reverse','backward differentiation')) + return string + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/balancethickness.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/balancethickness.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/balancethickness.py (revision 12168) @@ -0,0 +1,33 @@ +#module imports +from fielddisplay import fielddisplay +class balancethickness: + #properties + def __init__(self): + # {{{ Properties + self.spcthickness = float('NaN') + self.thickening_rate = float('NaN') + self.stabilization = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + + string=' balance thickness solution parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)')) + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0: None, 1: SU, 2: MacAyeal''s artificial diffusivity, 3:DG')) + return string + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #Type of stabilization used + obj.stabilization=1 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/basalforcings.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/basalforcings.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/basalforcings.py (revision 12168) @@ -0,0 +1,29 @@ +#module imports +from fielddisplay import fielddisplay + +class basalforcings: + #properties + def __init__(self): + # {{{ Properties + self.melting_rate = float('NaN') + self.melting_rate_correction = float('NaN') + self.geothermalflux = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" basal forcings parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"melting_rate","basal melting rate (positive if melting)")) + string="%s\n%s"%(string,fielddisplay(obj,"melting_rate_correction","additional melting applied when the grounding line retreats")) + string="%s\n%s"%(string,fielddisplay(obj,"geothermalflux","geothermal heat flux [W/m^2]")) + return string + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.m (revision 12168) @@ -2,5 +2,4 @@ % % Usage: -% cluster=generic('name','astrid',); % cluster=generic('name','astrid','np',3); % cluster=generic('name',oshostname(),'np',3,'login','username'); @@ -14,9 +13,9 @@ port=0; interactive=1; - codepath=[issmtier() '/bin']; - executionpath=[issmtier() '/execution']; - valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; - valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; - valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; + codepath=[issmdir() '/bin']; + executionpath=[issmdir() '/execution']; + valgrind=[issmdir() '/externalpackages/valgrind/install/bin/valgrind']; + valgrindlib=[issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so']; + valgrindsup=[issmdir() '/externalpackages/valgrind/issm.supp']; %}}} end @@ -28,6 +27,5 @@ %get name - if ~exist(options,'name'), error('option ''name'' has not been provided'); end - cluster.name=getfieldvalue(options,'name'); + cluster.name=getfieldvalue(options,'name',oshostname()); %initialize cluster using user settings if provided Index: /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/clusters/generic.py (revision 12168) @@ -0,0 +1,217 @@ +#GENERIC cluster class definition +# +# Usage: +# cluster=generic('name','astrid',); +# cluster=generic('name','astrid','np',3); +# cluster=generic('name',oshostname(),'np',3,'login','username'); + + +class generic: + #properties + def __init__(self): + # {{{ Properties + self.name='' + self.login='' + self.np=1 + self.port=0 + self.interactive=1 + self.codepath=issmdir() + '/bin' + self.executionpath=issmdir() + '/execution' + self.valgrind=issmdir() + '/externalpackages/valgrind/install/bin/valgrind' + self.valgrindlib=issmdir() + '/externalpackages/valgrind/install/lib/libmpidebug.so' + self.valgrindsup=issmdir() + '/externalpackages/valgrind/issm.supp' + #}}} + def __repr__(obj): + # {{{ Display + + string="class 'generic' object:" + string="%s\n\n%s"%(string,"%s%s"%(' name: ',obj.name)) + string="%s\n%s"%(string,"%s%i"%(' np: ',obj.np)) + string="%s\n%s"%(string,"%s%i"%(' port: ',obj.port)) + string="%s\n%s"%(string,"%s%s"%(' codepath: ',obj.codepath)) + string="%s\n%s"%(string,"%s%s"%(' executionpath: ',obj.executionpath)) + string="%s\n%s"%(string,"%s%s"%(' valgrind: ',obj.valgrind)) + string="%s\n%s"%(string,"%s%s"%(' valgrindlib: ',obj.valgrindlib)) + string="%s\n%s"%(string,"%s%s"%(' valgrindsup: ',obj.valgrindsup)) + return string + #}}} + + +#old matlab +# function cluster=generic(varargin) % {{{1 +# +# %use provided options to change fields +# options=pairoptions(varargin{:}); +# +# %get name +# if ~exist(options,'name'), error('option ''name'' has not been provided'); end +# cluster.name=getfieldvalue(options,'name'); +# +# %initialize cluster using user settings if provided +# if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end +# +# %OK get other fields +# for i=1:size(options.list,1), +# fieldname=options.list{i,1}; +# fieldvalue=options.list{i,2}; +# if ismember(fieldname,properties('generic')), +# cluster.(fieldname)=fieldvalue; +# else +# disp(['''' fieldname ''' is not a property of cluster generic']); +# end +# end +# end +# %}}} +# function checkconsistency(cluster,md,solution,analyses) % {{{1 +# if cluster.np<1 +# checkmessage(['number of processors should be at least 1']); +# end +# if isnan(cluster.np), +# checkessage('number of processors should not be NaN!'); +# end +# end +# %}}} +# function BuildQueueScript(cluster,md) % {{{1 +# +# %retrieve parameters +# modelname=md.miscellaneous.name; +# solution=md.private.solution; +# isvalgrind=md.debug.valgrind; +# isgprof=md.debug.gprof; +# +# %open file for writing: +# if ~ispc, +# fid=fopen([modelname '.queue'],'w'); +# else +# fid=fopen([modelname '.bat'],'w'); +# end +# +# %write instructions for launching a job on the cluster +# if ~ispc, +# fprintf(fid,'#!/bin/sh\n'); +# else +# fprintf(fid,'@echo off\n'); +# end +# +# if ~isvalgrind, +# if cluster.interactive +# if ~ispc, +# fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname); +# else +# fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname); +# end +# else +# if ~ispc, +# fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); +# else +# fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); +# end +# end +# else +# if ~ispc, +# %Add --gen-suppressions=all to get suppression lines +# fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); +# fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',... +# cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); +# else +# error('valgrind not supported on windows platforms'); +# end +# end +# +# if isgprof, +# if ~ispc, +# fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); +# else +# error('gprof not supported on windows platforms'); +# end +# +# end +# +# if ~md.settings.io_gather, +# if ~ispc, +# %concatenate the output files: +# fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); +# else +# error('iogather not supported on windows platforms'); +# end +# +# end +# +# %close file: +# fclose(fid); +# +# %in interactive mode, create a run file, and errlog and outlog file +# if cluster.interactive, +# fid=fopen([modelname '.errlog'],'w'); fclose(fid); +# fid=fopen([modelname '.outlog'],'w'); fclose(fid); +# end +# +# +# end +# %}}} +# function LaunchQueueJob(cluster,md,options)% {{{1 +# +# if ~ispc, +# %lauch command, to be executed via ssh +# launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.private.runtimename ' && mkdir ' md.private.runtimename ... +# ' && cd ' md.private.runtimename ' && mv ../' md.private.runtimename '.tar.gz ./ && tar -zxf ' md.private.runtimename '.tar.gz && source ' md.miscellaneous.name '.queue ']; +# +# if ~strcmpi(options.batch,'yes'), +# +# %compress the files into one zip. +# compressstring=['tar -zcf ' md.private.runtimename '.tar.gz ' md.miscellaneous.name '.bin ' md.miscellaneous.name '.queue ' md.miscellaneous.name '.petsc ']; +# if md.qmu.isdakota, +# compressstring=[compressstring md.miscellaneous.name '.qmu.in']; +# end +# if cluster.interactive, +# compressstring=[compressstring ' ' md.miscellaneous.name '.errlog ' md.miscellaneous.name '.outlog ']; +# end +# system(compressstring); +# +# disp('uploading input file and queueing script'); +# issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.private.runtimename '.tar.gz']}); +# +# disp('launching solution sequence on remote cluster'); +# issmssh(cluster.name,cluster.login,cluster.port,launchcommand); +# else +# disp('batch mode requested: not launching job interactively'); +# disp('launch solution sequence on remote cluster by hand'); +# end +# else +# %launch right here, do not compress or archive. +# system([md.miscellaneous.name '.bat']); +# end +# +# end %}}} +# function Download(cluster,md)% {{{1 +# +# if ~ispc, +# %some check +# if isempty(md.private.runtimename), +# error('supply runtime name for results to be loaded!'); +# end +# +# %Figure out the directory where all the files are in: +# directory=[cluster.executionpath '/' md.private.runtimename '/']; +# +# %What packages are we picking up from remote cluster +# packages={[md.miscellaneous.name '.outlog'],[md.miscellaneous.name '.errlog']}; +# if md.qmu.isdakota, +# packages{end+1}=[md.miscellaneous.name '.qmu.err']; +# packages{end+1}=[md.miscellaneous.name '.qmu.out']; +# if isfield(md.qmu.params,'tabular_graphics_data'), +# if md.qmu.params.tabular_graphics_data==true, +# packages{end+1}='dakota_tabular.dat'; +# end +# end +# else +# packages{end+1}=[md.miscellaneous.name '.outbin']; +# end +# +# %copy files from cluster to present directory +# issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); +# else +# %do nothing! +# end +# end %}}} +# Index: /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.m (revision 12168) @@ -12,18 +12,5 @@ methods function cluster=none(varargin) % {{{1 - cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); - end - %}}} - function disp(cluster) % {{{1 - % display the object - disp(sprintf('cluster class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); - disp(sprintf(' name: %s',cluster.name)); - end - %}}} - function checkconsistency(cluster,md,solution,analyses) % {{{1 - end - %}}} - function BuildQueueScript(cluster,md) % {{{1 - error('none.BuildQueueScript error message: serial cluster cannot build queue script'); + error('Cannot assign md.cluster to ''none'': ISSM is not available in serial model anymore'); end %}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/clusters/none.py (revision 12168) @@ -0,0 +1,24 @@ +#NONE cluster class definition +# +# Usage: +# cluster=none(); +# cluster=none('np',3); +# cluster=none('np',3,'login','username'); + +class none: + #properties + def __init__(self): + # {{{ Properties + self.name='none' + #}}} + def __repr__(obj): + # {{{ Display + + string="class 'none' object:" + string="%s\n\n%s"%(string,"%s%s"%(' name: ',obj.name)) + return string + #}}} + def checkconsistency(cluster,md,solution,analyses): + pass + def BuildQueueScript(cluster,md): + raise RuntimeError('none.BuildQueueScript error message: serial cluster cannot build queue script') Index: /issm/branches/trunk-jpl-damage/src/m/classes/constants.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/constants.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/constants.py (revision 12168) @@ -0,0 +1,41 @@ +#module imports +from fielddisplay import fielddisplay + +class constants: + #properties + def __init__(self): + # {{{ Properties + self.g = 0 + self.yts = 0 + self.referencetemperature = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" constants parameters:" + string="%s\n\n%s"%(string,fielddisplay(obj,"g","gravitational acceleration")) + string="%s\n%s"%(string,fielddisplay(obj,"yts","number of seconds in a year")) + string="%s\n%s"%(string,fielddisplay(obj,"referencetemperature","reference temperature used in the enthalpy model")) + + + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #acceleration due to gravity (m/s^2) + obj.g=9.81 + + #converstion from year to seconds + obj.yts=365*24*3600 + + #the reference temperature for enthalpy model (cf Aschwanden) + obj.referencetemperature=223.15 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/debug.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/debug.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/debug.py (revision 12168) @@ -0,0 +1,28 @@ +#module imports +from fielddisplay import fielddisplay + +class debug: + #properties + def __init__(self): + # {{{ Properties + self.valgrind=False + self.gprof = False + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" debug parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"valgrind","use Valgrind to debug (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"gprof","use gnu-profiler to find out where the time is spent")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.m (revision 12168) @@ -130,5 +130,5 @@ fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)'); fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)'); - fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice'); + fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice)'); disp(sprintf('\n %s','Rift options:')); Index: /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/diagnostic.py (revision 12168) @@ -0,0 +1,99 @@ +#module imports +from fielddisplay import fielddisplay + +class diagnostic: + #properties + def __init__(self): + # {{{ Properties + self.spcvx = float('NaN') + self.spcvy = float('NaN') + self.spcvz = float('NaN') + self.restol = 0 + self.reltol = 0 + self.abstol = 0 + self.isnewton = 0 + self.stokesreconditioning = 0 + self.viscosity_overshoot = 0 + self.icefront = float('NaN') + self.maxiter = 0 + self.shelf_dampening = 0 + self.vertex_pairing = float('NaN') + self.penalty_factor = float('NaN') + self.rift_penalty_lock = float('NaN') + self.rift_penalty_threshold = 0 + self.referential = float('NaN') + self.requested_outputs = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + + + string='\n Diagnostic solution parameters:' + string="%s\n\n%s"%(string,' Convergence criteria:') + + string="%s\n%s"%(string,fielddisplay(obj,'restol','mechanical equilibrium residual convergence criterion')) + string="%s\n%s"%(string,fielddisplay(obj,'reltol','velocity relative convergence criterion, NaN -> not applied')) + string="%s\n%s"%(string,fielddisplay(obj,'abstol','velocity absolute convergence criterion, NaN -> not applied')) + string="%s\n%s"%(string,fielddisplay(obj,'isnewton','Apply Newton''s method instead of a Picard fixed point method')) + string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of nonlinear iterations')) + string="%s\n%s"%(string,fielddisplay(obj,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)')) + + string="%s\n%s"%(string,' boundary conditions:') + + string="%s\n%s"%(string,fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice')) + + string="%s\n%s"%(string,' Rift options:') + string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_threshold','threshold for instability of mechanical constraints')) + string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_lock','number of iterations before rift penalties are locked')) + + string="%s\n%s"%(string,' Penalty options:') + string="%s\n%s"%(string,fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset')) + string="%s\n%s"%(string,fielddisplay(obj,'vertex_pairing','pairs of vertices that are penalized')) + + string="%s\n%s"%(string,' Other:') + string="%s\n%s"%(string,fielddisplay(obj,'shelf_dampening','use dampening for floating ice ? Only for Stokes model')) + string="%s\n%s"%(string,fielddisplay(obj,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model')) + string="%s\n%s"%(string,fielddisplay(obj,'referential','local referential')) + string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional outputs requested')) + + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + #maximum of non-linear iterations. + obj.maxiter=100 + + #Convergence criterion: absolute, relative and residual + obj.restol=10**-4; + obj.reltol=0.01 + obj.abstol=10 + + obj.stokesreconditioning=10**13 + obj.shelf_dampening=0 + + #Penalty factor applied kappa=max(stiffness matrix)*10^penalty_factor + obj.penalty_factor=3 + + #coefficient to update the viscosity between each iteration of + #a diagnostic according to the following formula + #viscosity(n)=viscosity(n)+viscosity_overshoot(viscosity(n)-viscosity(n-1)) + obj.viscosity_overshoot=0 + + #Stop the iterations of rift if below a threshold + obj.rift_penalty_threshold=0 + + #in some solutions, it might be needed to stop a run when only + #a few constraints remain unstable. For thermal computation, this + #parameter is often used. + obj.rift_penalty_lock=10 + + return obj + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/flaim.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/flaim.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/flaim.py (revision 12168) @@ -0,0 +1,50 @@ +#module imports +from fielddisplay import fielddisplay + +class flaim: + #properties + def __init__(self): + # {{{ Properties + self.targets = '' + self.tracks = '' + self.flightreqs = {} + self.criterion = float('NaN') + self.gridsatequator = 200000 + self.usevalueordering = True + self.split_antimeridian = True + self.solution = '' + self.quality = 0 + self.path_optimize = False + self.opt_ndir = 1 + self.opt_dist = 25 + self.opt_niter = 30000 + #}}} + def __repr__(obj): + # {{{ Displa + string=' FLAIM - Flight Line Adaptation using Ice sheet Modeling:' + + string="%s\n\n%s"%(string,' Input:') + string="%s\n%s"%(string,fielddisplay(obj,'targets' ,'name of kml output targets file ')) + string="%s\n%s"%(string,fielddisplay(obj,'tracks' ,'name of kml input tracks file ')) + string="%s\n%s"%(string,fielddisplay(obj,'flightreqs' ,'structure of kml flight requirements (not used yet)')) + string="%s\n%s"%(string,fielddisplay(obj,'criterion' ,'element or nodal criterion for flight path evaluation (metric)')) + + string="%s\n\n%s"%(string,' Arguments:') + string="%s\n%s"%(string,fielddisplay(obj,'gridsatequator' ,'number of grids at equator (determines resolution)')) + string="%s\n%s"%(string,fielddisplay(obj,'usevalueordering' ,'flag to consider target values for flight path evaluation')) + string="%s\n%s"%(string,fielddisplay(obj,'split_antimeridian' ,'flag to split polygons on the antimeridian')) + + string="%s\n\n%s"%(string,' Optimization:') + string="%s\n%s"%(string,fielddisplay(obj,'path_optimize' ,'optimize? (default false)')) + string="%s\n%s"%(string,fielddisplay(obj,'opt_ndir' ,['number of directions to test when moving a point. If this value = 1, a random direction is tested.',\ + 'A value > 1 results in directions equally spaced from [0, 2*PI] being tested.',\ + 'For example, 4 would result in directions [0, PI/2, PI, 3PI/2].'])) + string="%s\n%s"%(string,fielddisplay(obj,'opt_dist' ,'specifies the distance in km (default 25) to move a randomly selected path point on each iteration')) + string="%s\n%s"%(string,fielddisplay(obj,'opt_niter' ,['number of iterations (default 30,000) to run for flightplan optimization',\ + 'i.e. the number of times to randomly select a point and move it.'])) + + string="%s\n\n%s"%(string,' Output:') + string="%s\n%s"%(string,fielddisplay(obj,'solution' ,'name of kml solution file')) + string="%s\n%s"%(string,fielddisplay(obj,'quality' ,'quality of kml solution')) + return string + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/flowequation.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/flowequation.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/flowequation.py (revision 12168) @@ -0,0 +1,41 @@ +#module imports +from fielddisplay import fielddisplay + +class flowequation: + #properties + def __init__(self): + # {{{ Properties + + self.ismacayealpattyn = 0; + self.ishutter = 0; + self.isstokes = 0; + self.vertex_equation = float('NaN') + self.element_equation = float('NaN') + self.bordermacayeal = float('NaN') + self.borderpattyn = float('NaN') + self.borderstokes = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' flow equation parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'ismacayealpattyn','is the macayeal or pattyn approximation used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'ishutter','is the shallow ice approximation used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'isstokes','are the Full-Stokes equations used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'vertex_equation','flow equation for each vertex')) + string="%s\n%s"%(string,fielddisplay(obj,'element_equation','flow equation for each element')) + string="%s\n%s"%(string,fielddisplay(obj,'bordermacayeal','vertices on MacAyeal''s border (for tiling)')) + string="%s\n%s"%(string,fielddisplay(obj,'borderpattyn','vertices on Pattyn''s border (for tiling)')) + string="%s\n%s"%(string,fielddisplay(obj,'borderstokes','vertices on Stokes'' border (for tiling)')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/friction.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/friction.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/friction.py (revision 12168) @@ -0,0 +1,29 @@ +#module imports +from fielddisplay import fielddisplay + +class friction: + #properties + def __init__(self): + # {{{ Properties + self.coefficient = float('NaN') + self.p = float('NaN') + self.q = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string="Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p" + string="%s\n\n%s"%(string,fielddisplay(obj,"coefficient","friction coefficient [SI]")) + string="%s\n%s"%(string,fielddisplay(obj,"p","p exponent")) + string="%s\n%s"%(string,fielddisplay(obj,"q","q exponent")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/geometry.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/geometry.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/geometry.py (revision 12168) @@ -0,0 +1,35 @@ +#module imports +from fielddisplay import fielddisplay + +class geometry: + #properties + def __init__(self): + # {{{ Properties + self.surface = float('NaN') + self.thickness = float('NaN') + self.bed = float('NaN') + self.bathymetry = float('NaN') + self.hydrostatic_ratio = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + + string=" geometry parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,'surface','surface elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'thickness','ice thickness')) + string="%s\n%s"%(string,fielddisplay(obj,'bed','bed elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'bathymetry','bathymetry elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.m (revision 12168) @@ -37,5 +37,5 @@ end pos=find(md.mask.vertexongroundedice); - if any(md.geometry.bed(pos)-md.geometry.bathymetry(pos)), + if any(abs(md.geometry.bed(pos)-md.geometry.bathymetry(pos))>10^-10), checkmessage(['bathymetry not equal to bed on grounded ice !']); end Index: /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/groundingline.py (revision 12168) @@ -0,0 +1,34 @@ +#module imports +from fielddisplay import fielddisplay + +class groundingline: + #properties + def __init__(self): + # {{{ Properties + self.migration='' + self.melting_rate=float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' grounding line solution parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''')) + string="%s\n%s"%(string,fielddisplay(obj,'melting_rate','melting rate applied when previously grounded parts start floating')) + return string + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #Type of migration + obj.migration='None' + + #basal melting rate correction: + obj.melting_rate=0; + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/hydrology.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/hydrology.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/hydrology.py (revision 12168) @@ -0,0 +1,50 @@ +#module imports +from fielddisplay import fielddisplay + +class hydrology: + #properties + def __init__(self): + # {{{ Properties + self.spcwatercolumn = float('NaN') + self.n = 0 + self.CR = 0 + self.p = 0 + self.q = 0 + self.kn = 0 + self.stabilization = 0 + + #set defaults + self.setdefaultparameters() + + + #}}} + def __repr__(obj): + # {{{ Display + + string=' hydrology solution parameters:' + string="%s\n\n%s"%(string,fielddisplay(obj,'spcwatercolumn','water thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'n','Manning roughness coefficient')) + string="%s\n%s"%(string,fielddisplay(obj,'CR','tortuosity parameter')) + string="%s\n%s"%(string,fielddisplay(obj,'p','dimensionless exponent in Manning velocity formula')) + string="%s\n%s"%(string,fielddisplay(obj,'q','dimensionless exponent in Manning velocity formula')) + string="%s\n%s"%(string,fielddisplay(obj,'kn','parameter in effective pressure formula')) + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #Parameters from Johnson's 2002 thesis, section 3.5.4 + obj.n=.02 + obj.CR=.01 + obj.p=2 + obj.q=1 + obj.kn=0 + + #Type of stabilization to use 0:nothing 1:artificial_diffusivity + obj.stabilization=1 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/initialization.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/initialization.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/initialization.py (revision 12168) @@ -0,0 +1,42 @@ +#module imports +from fielddisplay import fielddisplay + +class initialization: + #properties + def __init__(self): + # {{{ Properties + + self.vx = float('NaN') + self.vy = float('NaN') + self.vz = float('NaN') + self.vel = float('NaN') + self.pressure = float('NaN') + self.temperature = float('NaN') + self.watercolumn = float('NaN') + self.waterfraction = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' initial field values:' + + string="%s\n%s"%(string,fielddisplay(obj,'vx','x component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vy','y component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vz','z component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vel','velocity norm')) + string="%s\n%s"%(string,fielddisplay(obj,'pressure','pressure field')) + string="%s\n%s"%(string,fielddisplay(obj,'temperature','temperature in Kelvins')) + string="%s\n%s"%(string,fielddisplay(obj,'watercolumn','thickness of subglacial water')) + string="%s\n%s"%(string,fielddisplay(obj,'waterfraction','fraction of water in the ice')) + + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/inversion.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/inversion.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/inversion.py (revision 12168) @@ -0,0 +1,104 @@ +#module imports +from fielddisplay import fielddisplay + +class inversion: + #properties + def __init__(self): + # {{{ Properties + self.iscontrol = 0 + self.tao = 0 + self.incomplete_adjoint = 0 + self.control_parameters = float('NaN') + self.nsteps = 0 + self.maxiter_per_step = float('NaN') + self.cost_functions = float('NaN') + self.cost_functions_coefficients = float('NaN') + self.gradient_scaling = float('NaN') + self.cost_function_threshold = 0 + self.min_parameters = float('NaN') + self.max_parameters = float('NaN') + self.step_threshold = float('NaN') + self.gradient_only = 0 + self.vx_obs = float('NaN') + self.vy_obs = float('NaN') + self.vz_obs = float('NaN') + self.vel_obs = float('NaN') + self.thickness_obs = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string='\n Inversion parameters:' + string="%s\n%s"%(string,fielddisplay(obj,'iscontrol','is inversion activated?')) + string="%s\n%s"%(string,fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?')) + string="%s\n%s"%(string,fielddisplay(obj,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}')) + string="%s\n%s"%(string,fielddisplay(obj,'nsteps','number of optimization searches')) + string="%s\n%s"%(string,fielddisplay(obj,'cost_functions','indicate the type of response for each optimization step')) + string="%s\n%s"%(string,fielddisplay(obj,'cost_functions_coefficients','cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter')) + string="%s\n%s"%(string,fielddisplay(obj,'cost_function_threshold','misfit convergence criterion. Default is 1%, NaN if not applied')) + string="%s\n%s"%(string,fielddisplay(obj,'maxiter_per_step','maximum iterations during each optimization step')) + string="%s\n%s"%(string,fielddisplay(obj,'gradient_scaling','scaling factor on gradient direction during optimization, for each optimization step')) + string="%s\n%s"%(string,fielddisplay(obj,'step_threshold','decrease threshold for misfit, default is 30%')) + string="%s\n%s"%(string,fielddisplay(obj,'min_parameters','absolute minimum acceptable value of the inversed parameter on each vertex')) + string="%s\n%s"%(string,fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex')) + string="%s\n%s"%(string,fielddisplay(obj,'gradient_only','stop control method solution at gradient')) + string="%s\n%s"%(string,fielddisplay(obj,'vx_obs','observed velocity x component [m/a]')) + string="%s\n%s"%(string,fielddisplay(obj,'vy_obs','observed velocity y component [m/a]')) + string="%s\n%s"%(string,fielddisplay(obj,'vel_obs','observed velocity magnitude [m/a]')) + string="%s\n%s"%(string,fielddisplay(obj,'thickness_obs','observed thickness [m]')) + string="%s\n%s"%(string,'Available cost functions:') + string="%s\n%s"%(string,' 101: SurfaceAbsVelMisfit') + string="%s\n%s"%(string,' 102: SurfaceRelVelMisfit') + string="%s\n%s"%(string,' 103: SurfaceLogVelMisfit') + string="%s\n%s"%(string,' 104: SurfaceLogVxVyMisfit') + string="%s\n%s"%(string,' 105: SurfaceAverageVelMisfit') + string="%s\n%s"%(string,' 201: ThicknessAbsMisfit') + string="%s\n%s"%(string,' 501: DragCoefficientAbsGradient') + string="%s\n%s"%(string,' 502: RheologyBbarAbsGradient') + string="%s\n%s"%(string,' 503: ThicknessAbsGradient') + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #default is incomplete adjoint for now + obj.incomplete_adjoint=1 + + #parameter to be inferred by control methods (only + #drag and B are supported yet) + obj.control_parameters=['FrictionCoefficient'] + + #number of steps in the control methods + obj.nsteps=20 + + #maximum number of iteration in the optimization algorithm for + #each step + obj.maxiter_per_step=20*ones(obj.nsteps) + + #the inversed parameter is updated as follows: + #new_par=old_par + gradient_scaling(n)*C*gradient with C in [0 1]; + #usually the gradient_scaling must be of the order of magnitude of the + #inversed parameter (10^8 for B, 50 for drag) and can be decreased + #after the first iterations + obj.gradient_scaling=50*ones(obj.nsteps) + + #several responses can be used: + obj.cost_functions=101*ones(obj.nsteps) + + #step_threshold is used to speed up control method. When + #misfit(1)/misfit(0) < obj.step_threshold, we go directly to + #the next step + obj.step_threshold=.7*ones(obj.nsteps) #30 per cent decrement + + #stop control solution at the gradient computation and return it? + obj.gradient_only=0 + + #cost_function_threshold is a criteria to stop the control methods. + #if J[n]-J[n-1]/J[n] < criteria, the control run stops + #NaN if not applied + obj.cost_function_threshold=NaN #not activated + + return obj + #}}} + + Index: /issm/branches/trunk-jpl-damage/src/m/classes/mask.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/mask.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/mask.py (revision 12168) @@ -0,0 +1,36 @@ +#module imports +from fielddisplay import fielddisplay + +class mask: + #properties + def __init__(self): + # {{{ Properties + self.elementonfloatingice = float('NaN') + self.elementongroundedice = float('NaN') + self.elementonwater = float('NaN') + self.vertexonfloatingice = float('NaN') + self.vertexongroundedice = float('NaN') + self.vertexonwater = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + + string=""; + string="%s\n%s"%(string,fielddisplay(obj,"elementonfloatingice","element on floating ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonfloatingice","vertex on floating ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementongroundedice","element on grounded ice list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexongroundedice","vertex on grounded ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonwater","element on water flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonwater","vertex on water flags list")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/materials.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/materials.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/materials.py (revision 12168) @@ -0,0 +1,80 @@ +#module imports +from fielddisplay import fielddisplay + +class materials: + #properties + def __init__(self): + # {{{ Properties + self.rho_ice = 0; + self.rho_water = 0; + self.mu_water = 0; + self.heatcapacity = 0; + self.latentheat = 0; + self.thermalconductivity = 0; + self.meltingpoint = 0; + self.beta = 0; + self.mixed_layer_capacity = 0; + self.thermal_exchange_velocity = 0; + self.rheology_B = float('NaN') + self.rheology_n = float('NaN') + self.rheology_law = ""; + + self.setdefaultparameters() + #}}} + def __repr__(obj): + # {{{ Display + string=" Materials:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"rho_ice","ice density [kg/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"rho_water","water density [kg/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"mu_water","water viscosity [N s/m^2]")) + string="%s\n%s"%(string,fielddisplay(obj,"heatcapacity","heat capacity [J/kg/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"thermalconductivity","ice thermal conductivity [W/m/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"meltingpoint","melting point of ice at 1atm in K")) + string="%s\n%s"%(string,fielddisplay(obj,"latentheat","latent heat of fusion [J/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"beta","rate of change of melting point with pressure [K/Pa]")) + string="%s\n%s"%(string,fielddisplay(obj,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"thermal_exchange_velocity","thermal exchange velocity [m/s]")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_B","flow law parameter [Pa/s^(1/n)]")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_n","Glen""s flow law exponent")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_law","law for the temperature dependance of the rheology: ""None"", ""Paterson"" or ""Arrhenius""")) + + return string + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters + #ice density (kg/m^3) + obj.rho_ice=917 + + #water density (kg/m^3) + obj.rho_water=1023 + + #water viscosity (N.s/m^2) + obj.mu_water=0.001787 + + #ice heat capacity cp (J/kg/K) + obj.heatcapacity=2093 + + #ice latent heat of fusion L (J/kg) + obj.latentheat=3.34*10**5 + + #ice thermal conductivity (W/m/K) + obj.thermalconductivity=2.4 + + #the melting point of ice at 1 atmosphere of pressure in K + obj.meltingpoint=273.15 + + #rate of change of melting point with pressure (K/Pa) + obj.beta=9.8*10**-8 + + #mixed layer (ice-water interface) heat capacity (J/kg/K) + obj.mixed_layer_capacity=3974 + + #thermal exchange velocity (ice-water interface) (m/s) + obj.thermal_exchange_velocity=1.00*10**-4 + + #Rheology law: what is the temperature dependence of B with T + #available: none, paterson and arrhenius + obj.rheology_law='Paterson' + return obj + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/mesh.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/mesh.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/mesh.py (revision 12168) @@ -0,0 +1,125 @@ +#module imports +from fielddisplay import fielddisplay + +class mesh: + #properties + def __init__(self): + # {{{ Properties + self.x = float('NaN'); + self.y = float('NaN'); + self.z = float('NaN'); + self.elements = float('NaN'); + self.dimension = 0; + self.numberoflayers = 0; + self.numberofelements = 0; + self.numberofvertices = 0; + self.numberofedges = 0; + + self.lat = float('NaN'); + self.long = float('NaN'); + self.hemisphere = float('NaN'); + + self.elementonbed = float('NaN'); + self.elementonsurface = float('NaN'); + self.vertexonbed = float('NaN'); + self.vertexonsurface = float('NaN'); + self.lowerelements = float('NaN'); + self.lowervertex = float('NaN'); + self.upperelements = float('NaN'); + self.uppervertex = float('NaN'); + self.vertexonboundary = float('NaN'); + + self.edges = float('NaN'); + self.segments = float('NaN'); + self.segmentmarkers = float('NaN'); + self.vertexconnectivity = float('NaN'); + self.elementconnectivity = float('NaN'); + self.average_vertex_connectivity = 0; + + self.x2d = float('NaN'); + self.y2d = float('NaN'); + self.elements2d = float('NaN'); + self.numberofvertices2d = 0; + self.numberofelements2d = 0; + + self.extractedvertices = float('NaN'); + self.extractedelements = float('NaN'); + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + + if obj.dimension==3: + string="\n%s"%(" Elements and vertices of the original 2d mesh:") + + string="%s\n%s"%(string,fielddisplay(obj,"numberofelements2d","number of elements")) + string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices2d","number of vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"elements2d","index into (x,y,z), coordinates of the vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"x2d","vertices x coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"y2d","vertices y coordinate")) + + string="%s\n%s" %(string,"Elements and vertices of the extruded 3d mesh:") + else: + string="\n%s"%(" Elements and vertices:") + + string="%s\n%s"%(string,fielddisplay(obj,"numberofelements","number of elements")) + + + + + string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices","number of vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"elements","index into (x,y,z), coordinates of the vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"x","vertices x coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"y","vertices y coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"z","vertices z coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)")) + string="%s\n%s"%(string,fielddisplay(obj,"numberofedges","number of edges of the 2d mesh")) + + string="%s%s"%(string,"\n Properties:") + + string="%s\n%s"%(string,fielddisplay(obj,"dimension","mesh dimension (2d or 3d)")) + string="%s\n%s"%(string,fielddisplay(obj,"numberoflayers","number of extrusion layers")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonbed","lower vertices flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonbed","lower elements flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonsurface","upper vertices flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonsurface","upper elements flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"uppervertex","upper vertex list (NaN for vertex on the upper surface)")) + string="%s\n%s"%(string,fielddisplay(obj,"upperelements","upper element list (NaN for element on the upper layer)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowervertex","lower vertex list (NaN for vertex on the lower surface)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowerelements","lower element list (NaN for element on the lower layer")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonboundary","vertices on the boundary of the domain flag list")) + + string="%s\n%s"%(string,fielddisplay(obj,"segments","edges on domain boundary (vertex1 vertex2 element)")) + string="%s\n%s"%(string,fielddisplay(obj,"segmentmarkers","number associated to each segment")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexconnectivity","list of vertices connected to vertex_i")) + string="%s\n%s"%(string,fielddisplay(obj,"elementconnectivity","list of vertices connected to element_i")) + string="%s\n%s"%(string,fielddisplay(obj,"average_vertex_connectivity","average number of vertices connected to one vertex")) + + string="%s%s"%(string,"\n Extracted model:") + + string="%s\n%s"%(string,fielddisplay(obj,"extractedvertices","vertices extracted from the model")) + string="%s\n%s"%(string,fielddisplay(obj,"extractedelements","elements extracted from the model")) + + string="%s%s"%(string,"\n Projection:") + string="%s\n%s"%(string,fielddisplay(obj,"lat","vertices latitude")) + string="%s\n%s"%(string,fielddisplay(obj,"long","vertices longitude")) + string="%s\n%s"%(string,fielddisplay(obj,"hemisphere","Indicate hemisphere ""n"" or ""s"" ")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #the connectivity is the avergaded number of nodes linked to a + #given node through an edge. This connectivity is used to initially + #allocate memory to the stiffness matrix. A value of 16 seems to + #give a good memory/time ration. This value can be checked in + #trunk/test/Miscellaneous/runme.m + obj.average_vertex_connectivity=25 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/miscellaneous.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/miscellaneous.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/miscellaneous.py (revision 12168) @@ -0,0 +1,30 @@ +#module imports +from fielddisplay import fielddisplay + +class miscellaneous: + #properties + def __init__(self): + # {{{ Properties + self.notes = '' + self.name = '' + self.dummy = {} + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' miscellaneous parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'notes','notes in a cell of strings')) + string="%s\n%s"%(string,fielddisplay(obj,'name','model name')) + string="%s\n%s"%(string,fielddisplay(obj,'dummy','empty field to store some data')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/model.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/model.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/model.py (revision 12168) @@ -0,0 +1,114 @@ +#module imports {{{ +from mesh import mesh +from mask import mask +from geometry import geometry +from constants import constants +from surfaceforcings import surfaceforcings +from basalforcings import basalforcings +from materials import materials +from friction import friction +from flowequation import flowequation +from timestepping import timestepping +from initialization import initialization +from rifts import rifts +from debug import debug +from verbose import verbose +from settings import settings +from solver import solver +from none import none +from balancethickness import balancethickness +from diagnostic import diagnostic +from groundingline import groundingline +from hydrology import hydrology +from prognostic import prognostic +from thermal import thermal +from steadystate import steadystate +from transient import transient +from autodiff import autodiff +from flaim import flaim +from inversion import inversion +from qmu import qmu +from radaroverlay import radaroverlay +from miscellaneous import miscellaneous +from private import private +#}}} +class model: + #properties + def __init__(self): + # {{{ Properties + self.mesh = mesh() + self.mask = mask() + self.geometry = geometry() + self.constants = constants() + self.surfaceforcings = surfaceforcings() + self.basalforcings = basalforcings() + self.materials = materials() + self.friction = friction() + self.flowequation = flowequation() + self.timestepping = timestepping() + self.initialization = initialization() + self.rifts = rifts() + + self.debug = debug() + self.verbose = verbose() + self.settings = settings() + self.solver = solver() + self.cluster = none() + + self.balancethickness = balancethickness() + self.diagnostic = diagnostic() + self.groundingline = groundingline() + self.hydrology = hydrology() + self.prognostic = prognostic() + self.thermal = thermal() + self.steadystate = steadystate() + self.transient = transient() + + self.autodiff = autodiff() + self.flaim = flaim() + self.inversion = inversion() + self.qmu = qmu() + + self.results = []; + self.radaroverlay = radaroverlay() + self.miscellaneous = miscellaneous() + self.private = private() + #}}} + def __repr__(obj): + # {{{ Display + + #print "Here %s the number: %d" % ("is", 37) + string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties") + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("mask","[%s,%s]" % ("1x1",obj.mask.__class__.__name__),"defines grounded and floating elements")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("geometry","[%s,%s]" % ("1x1",obj.geometry.__class__.__name__),"surface elevation, bedrock topography, ice thickness,...")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("constants","[%s,%s]" % ("1x1",obj.constants.__class__.__name__),"physical constants")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("surfaceforcings","[%s,%s]" % ("1x1",obj.surfaceforcings.__class__.__name__),"surface forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("basalforcings","[%s,%s]" % ("1x1",obj.basalforcings.__class__.__name__),"bed forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("materials","[%s,%s]" % ("1x1",obj.materials.__class__.__name__),"material properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("friction","[%s,%s]" % ("1x1",obj.friction.__class__.__name__),"basal friction/drag properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flowequation","[%s,%s]" % ("1x1",obj.flowequation.__class__.__name__),"flow equations")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("timestepping","[%s,%s]" % ("1x1",obj.timestepping.__class__.__name__),"time stepping for transient models")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("initialization","[%s,%s]" % ("1x1",obj.initialization.__class__.__name__),"initial guess/state")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("rifts","[%s,%s]" % ("1x1",obj.rifts.__class__.__name__),"rifts properties'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("debug","[%s,%s]" % ("1x1",obj.debug.__class__.__name__),"debugging tools (valgrind, gprof")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("solver","[%s,%s]" % ("1x1",obj.solver.__class__.__name__),"PETSc options for each solution'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("diagnostic","[%s,%s]" % ("1x1",obj.diagnostic.__class__.__name__),"parameters for diagnostic solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("groundingline","[%s,%s]" % ("1x1",obj.groundingline.__class__.__name__),"parameters for groundingline solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("hydrology","[%s,%s]" % ("1x1",obj.hydrology.__class__.__name__),"parameters for hydrology solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("prognostic","[%s,%s]" % ("1x1",obj.prognostic.__class__.__name__),"parameters for prognostic solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("thermal","[%s,%s]" % ("1x1",obj.thermal.__class__.__name__),"parameters for thermal solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("steadystate","[%s,%s]" % ("1x1",obj.steadystate.__class__.__name__),"parameters for steadystate solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("transient","[%s,%s]" % ("1x1",obj.transient.__class__.__name__),"parameters for transient solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("autodiff","[%s,%s]" % ("1x1",obj.autodiff.__class__.__name__),"automatic differentiation parameters")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flaim","[%s,%s]" % ("1x1",obj.flaim.__class__.__name__),"flaim parameters")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) + return string; + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m (revision 12168) @@ -382,5 +382,5 @@ md.solver = addoptions(md.solver,DiagnosticVertAnalysisEnum,iluasmoptions); end - md.cluster = none(); + md.cluster = generic(); md.balancethickness = balancethickness(); md.diagnostic = diagnostic(); Index: /issm/branches/trunk-jpl-damage/src/m/classes/modellist.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/modellist.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/modellist.m (revision 12168) @@ -7,5 +7,5 @@ properties (SetAccess=public) models = cell(0,1); - cluster = none(); + cluster = generic(); end methods Index: /issm/branches/trunk-jpl-damage/src/m/classes/pairoptions.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/pairoptions.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/pairoptions.py (revision 12168) @@ -0,0 +1,38 @@ +class pairoptions: + #properties + def __init__(self,*args): + # {{{ Properties + if len(args)%2==1: + raise RuntimeError('pairoption error message: an even number of options is required') + + #create a pairoption object + if len(args)==0: + self.list=[] + else: + self.list=[] + for i in range(int(round(len(args)/2))): + if isinstance(args[2*i],str): + self.list.append([args[2*i],args[2*i+1]]) + else: + #option is not a string, ignore it + print("%s%i%s"%('buildlist info: option number ',i,' is not a string, it will be ignored')) + continue + + #}}} + def __repr__(obj): + # {{{ Display + if not obj.list: + string=' list: empty' + else: + string=" list: (%i)"%(len(obj.list)) + for i in range(len(obj.list)): + if isinstance(obj.list[i][1],str): + string2=" field: %-10s value: '%s'"%(obj.list[i][0],obj.list[i][1]) + elif isinstance(obj.list[i][1],float): + string2=" field: %-10s value: %g"%(obj.list[i][0],obj.list[i][1]) + elif isinstance(obj.list[i][1],int): + string2=" field: %-10s value: %i"%(obj.list[i][0],obj.list[i][1]) + else: + string2=" field: %-10s value: (%i)"%(len(obj.list[i][1])) + string="%s\n%s"%(string,string2) + return string Index: /issm/branches/trunk-jpl-damage/src/m/classes/private.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/private.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/private.py (revision 12168) @@ -0,0 +1,29 @@ +#module imports +from fielddisplay import fielddisplay + +class private: + #properties + def __init__(self): + # {{{ Properties + self.runtimename = '' + self.bamg = {} + self.solution = ''; + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' private parameters: do not change' + string="%s\n%s"%(string,fielddisplay(obj,'runtimename','name of the run launched')) + string="%s\n%s"%(string,fielddisplay(obj,'bamg','structure with mesh properties construced if bamg is used to mesh the domain')) + string="%s\n%s"%(string,fielddisplay(obj,'solution','type of solution launched')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/prognostic.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/prognostic.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/prognostic.py (revision 12168) @@ -0,0 +1,47 @@ +#module imports +from fielddisplay import fielddisplay + +class prognostic: + #properties + def __init__(self): + # {{{ Properties + self.spcthickness = float('NaN') + self.min_thickness = 0 + self.hydrostatic_adjustment = 0 + self.stabilization = 0 + self.vertex_pairing = float('NaN') + self.penalty_factor = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' Prognostic solution parameters:' + string="%s\n\n%s"%(string,fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'min_thickness','minimum ice thickness allowed')) + string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ')) + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin')) + + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin + obj.stabilization=1 + + #Factor applied to compute the penalties kappa=max(stiffness matrix)*10^penalty_factor + obj.penalty_factor=3 + + #Minimum ice thickness that can be used + obj.min_thickness=1 + + #Hydrostatic adjustment + obj.hydrostatic_adjustment='Absolute' + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/qmu.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/qmu.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/qmu.py (revision 12168) @@ -0,0 +1,39 @@ +#module imports +from fielddisplay import fielddisplay + +class qmu: + #properties + def __init__(self): + # {{{ Properties + self.isdakota = 0 + self.variables = {} + self.responses = {} + self.method = {} + self.params = {} + self.results = {} + self.partition = float('NaN') + self.numberofpartitions = 0 + self.numberofresponses = 0 + self.variabledescriptors = [] + self.responsedescriptors = [] + self.mass_flux_profile_directory = float('NaN') + self.mass_flux_profiles = float('NaN') + self.mass_flux_segments = [] + self.adjacency = float('NaN') + self.vertex_weight = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" qmu parameters: not implemented yet!" + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/radaroverlay.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/radaroverlay.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/radaroverlay.py (revision 12168) @@ -0,0 +1,29 @@ +#module imports +from fielddisplay import fielddisplay + +class radaroverlay: + #properties + def __init__(self): + # {{{ Properties + self.pwr = float('NaN') + self.x = float('NaN') + self.y = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' radaroverlay parameters:' + string="%s\n\n%s"%(string,fielddisplay(obj,'pwr','radar power image (matrix)')) + string="%s\n%s"%(string,fielddisplay(obj,'x','corresponding x coordinates')) + string="%s\n%s"%(string,fielddisplay(obj,'y','corresponding y coordinates')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/rifts.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/rifts.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/rifts.py (revision 12168) @@ -0,0 +1,28 @@ +#module imports +from fielddisplay import fielddisplay + +class rifts: + #properties + def __init__(self): + # {{{ Properties + self.riftstruct = float('NaN') + self.riftproperties = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' rifts parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'riftstruct','structure containing all rift information (vertices coordinates, segments, type of melange, ...)')) + string="%s\n%s"%(string,fielddisplay(obj,'riftproperties','')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/settings.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/settings.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/settings.py (revision 12168) @@ -0,0 +1,53 @@ +#module imports +from fielddisplay import fielddisplay + +class settings: + #properties + def __init__(self): + # {{{ Properties + self.io_gather = 0 + self.lowmem = 0 + self.results_as_patches = 0 + self.output_frequency = 0 + self.waitonlock = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" general settings parameters:" + + string="%s\n%s"%(string,fielddisplay(obj,"io_gather","I/O gathering strategy for result outputs (default 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowmem","is the memory limited ? (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"results_as_patches","provide results as patches for each element (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"output_frequency","frequency at which results are saved in all solutions with multiple time_steps")) + string="%s\n%s"%(string,fielddisplay(obj,"waitonlock","maximum number of minutes to wait for batch results, or return 0")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #are we short in memory ? (0 faster but requires more memory) + obj.lowmem=0 + + #i/o: + obj.io_gather=1 + + #results frequency by default every step + obj.output_frequency=1 + + #do not use patches by default (difficult to plot) + obj.results_as_patches=0 + + #this option can be activated to load automatically the results + #onto the model after a parallel run by waiting for the lock file + #N minutes that is generated once the solution has converged + #0 to desactivate + obj.waitonlock=float('Inf') + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/solver.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/solver.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/classes/solver.m (revision 12168) @@ -18,5 +18,8 @@ end end % }}} - function obj = addoptions(obj,analysis,solveroptions) % {{{1 + function obj = addoptions(obj,analysis,varargin) % {{{1 + % Usage example: + % md.solver=addoptions(md.solver,DiagnosticHorizAnalysisEnum,stokesoptions()); + % md.solver=addoptions(md.solver,DiagnosticHorizAnalysisEnum); %Convert analysis from enum to string @@ -29,5 +32,5 @@ %Add solver options to analysis - obj.(analysis) = solveroptions; + if nargin==3, obj.(analysis) = varargin{1}; end end %}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/solver.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/solver.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/solver.py (revision 12168) @@ -0,0 +1,49 @@ +#module imports {{{ +import fielddisplay +import ismumps +from mumpsoptions import * +from iluasmoptions import * +#}}} +class solver: + #properties + def __init__(self): + # {{{ Properties + if ismumps: + self.options=[["NoneAnalysis",mumpsoptions()]] + else: + self.options=[["NoneAnalysis",iluasmoptions()]] + #}}} + def __repr__(obj): + # {{{ Display + + string2=" solver parameters:" + for i in range(len(obj.options)): + option=obj.options[i] + analysis=option[0] + ioptions=option[1] + + string="" + for i in range(len(ioptions)): + option=ioptions[i] + if not option: + #do nothing + pass + elif len(option)==1: + #this option has only one argument + string="%s%s%s"%(string," -",option[0]) + elif len(option)==2: + #option with value. value can be string or scalar + if isinstance(option[1],float): + string="%s%s%s%s%s"%(string," -",option[0]," ","%g"%(option[1])) + elif isinstance(option[1],str): + string="%s%s%s%s%s"%(string," -",option[0]," ",option[1]) + elif isinstance(option[1],int): + string="%s%s%s%s%s"%(string," -",option[0]," ","%i"%(option[1])) + else: + raise RuntimeError("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) + else: + raise RuntimeError("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) + + string2="%s\n%s"%(string2," %s -> '%s'"%(analysis,string)) + return string2 + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/steadystate.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/steadystate.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/steadystate.py (revision 12168) @@ -0,0 +1,36 @@ +#module imports +from fielddisplay import fielddisplay + +class steadystate: + #properties + def __init__(self): + # {{{ Properties + self.reltol = 0 + self.maxiter = 0 + self.requested_outputs = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' steadystate solution parameters:' + string="%s\n%s"%(string,fielddisplay(obj,'reltol','relative tolerance criterion')) + string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of iterations')) + string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional requested outputs')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #maximum of steady state iterations + obj.maxiter=100 + + #Relative tolerance for the steadystate convertgence + obj.reltol=0.01 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/surfaceforcings.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/surfaceforcings.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/surfaceforcings.py (revision 12168) @@ -0,0 +1,29 @@ +#module imports +from fielddisplay import fielddisplay + +class surfaceforcings: + #properties + def __init__(self): + # {{{ Properties + self.precipitation = float('NaN') + self.mass_balance = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" surface forcings parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,'precipitation','surface precipitation [m/yr water eq]')) + string="%s\n%s"%(string,fielddisplay(obj,'mass_balance','surface mass balance [m/yr ice eq]')) + + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/thermal.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/thermal.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/thermal.py (revision 12168) @@ -0,0 +1,52 @@ +#module imports +from fielddisplay import fielddisplay + +class thermal: + #properties + def __init__(self): + # {{{ Properties + self.spctemperature = float('NaN') + self.penalty_threshold = 0 + self.stabilization = 0 + self.maxiter = 0 + self.penalty_lock = 0 + self.penalty_factor = 0 + self.isenthalpy = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' Thermal solution parameters:' + string="%s\n\n%s"%(string,fielddisplay(obj,'spctemperature','temperature constraints (NaN means no constraint)')) + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->SUPG')) + string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of non linear iterations')) + string="%s\n%s"%(string,fielddisplay(obj,'penalty_lock','stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)')) + string="%s\n%s"%(string,fielddisplay(obj,'penalty_threshold','threshold to declare convergence of thermal solution (default is 0)')) + string="%s\n%s"%(string,fielddisplay(obj,'isenthalpy','use an enthalpy formulation to include temperate ice (default is 0)')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #Number of unstable constraints acceptable + obj.penalty_threshold=0 + + #Type of stabilization used + obj.stabilization=1 + + #Maximum number of iterations + obj.maxiter=100 + + #factor used to compute the values of the penalties: kappa=max(stiffness matrix)*10^penalty_factor + obj.penalty_factor=3 + + #Should we use cold ice (default) or enthalpy formulation + obj.isenthalpy=0 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/timestepping.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/timestepping.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/timestepping.py (revision 12168) @@ -0,0 +1,41 @@ +#module imports +from fielddisplay import fielddisplay + +class timestepping: + #properties + def __init__(self): + # {{{ Properties + self.time_step = 0 + self.final_time = 0 + self.time_adapt = 0 + self.cfl_coefficient = 0 + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=" timestepping parameters:" + string="%s\n\n%s"%(string,fielddisplay(obj,"time_step","length of time steps [yrs]")) + string="%s\n%s"%(string,fielddisplay(obj,"final_time","final time to stop the simulation [yrs]")) + string="%s\n%s"%(string,fielddisplay(obj,"time_adapt","use cfl condition to define time step ? (0 or 1) ")) + string="%s\n%s"%(string,fielddisplay(obj,"cfl_coefficient","coefficient applied to cfl condition")) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #time between 2 time steps + obj.time_step=1/2 + + #final time + obj.final_time=10*obj.time_step + + #time adaptation? + obj.time_adapt=0 + obj.cfl_coefficient=.5 + + return obj + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/classes/transient.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/transient.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/transient.py (revision 12168) @@ -0,0 +1,40 @@ +#module imports +from fielddisplay import fielddisplay + +class transient: + #properties + def __init__(self): + # {{{ Properties + self.isprognostic = 0 + self.isdiagnostic = 0 + self.isthermal = 0 + self.isgroundingline = 0 + self.requested_outputs = float('NaN') + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(obj): + # {{{ Display + string=' transient solution parameters:' + string="%s\n%s"%(string,fielddisplay(obj,'isprognostic','indicates if a prognostic solution is used in the transient')) + string="%s\n%s"%(string,fielddisplay(obj,'isthermal','indicates if a thermal solution is used in the transient')) + string="%s\n%s"%(string,fielddisplay(obj,'isdiagnostic','indicates if a diagnostic solution is used in the transient')) + string="%s\n%s"%(string,fielddisplay(obj,'isgroundingline','indicates if a groundingline migration is used in the transient')) + string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','list of additional outputs requested')) + return string + #}}} + + def setdefaultparameters(obj): + # {{{setdefaultparameters + + #full analysis: Diagnostic, Prognostic and Thermal but no groundingline migration for now + obj.isprognostic=1 + obj.isdiagnostic=1 + obj.isthermal=1 + obj.isgroundingline=0 + + return obj + #}}} + Index: /issm/branches/trunk-jpl-damage/src/m/classes/verbose.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/verbose.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/classes/verbose.py (revision 12168) @@ -0,0 +1,27 @@ +#module imports +from fielddisplay import fielddisplay + +class verbose: + #properties + def __init__(self): + # {{{ Properties + self.mprocessor = False + self.module = False + self.solution = False + self.solver = False + self.convergence = False + self.control = False + self.qmu = False + #}}} + def __repr__(obj): + # {{{ Display + string="%s%s%s\n\n"%("class '",obj.__class__.__name__,"'=") + string="%s%s\n"%(string," %15s : %s"%("mprocessor",obj.mprocessor)) + string="%s%s\n"%(string," %15s : %s"%("module",obj.module)) + string="%s%s\n"%(string," %15s : %s"%("solution",obj.solution)) + string="%s%s\n"%(string," %15s : %s"%("solver",obj.solver)) + string="%s%s\n"%(string," %15s : %s"%("convergence",obj.convergence)) + string="%s%s\n"%(string," %15s : %s"%("control",obj.control)) + string="%s%s\n"%(string," %15s : %s"%("qmu",obj.qmu)) + return string + #}}} Index: /issm/branches/trunk-jpl-damage/src/m/kml/README.txt =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/README.txt (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/kml/README.txt (revision 12168) @@ -61,5 +61,5 @@ There are some other utilities that are used in the construction of topological tables for the kml writing. -nodeconnectivity.m - create a node connectivity table (nnodes x mxepg+1) +kmlnodeconnectivity.m - create a node connectivity table (nnodes x mxepg+1) edgeadjacency.m - create an edge adjacency array (elems x edges) edgeperimeter.m - create an edge perimeter (edgeper x 2) and element perimeter (edgeper x 1) list Index: /issm/branches/trunk-jpl-damage/src/m/kml/kml_part_edges.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/kml_part_edges.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/kml/kml_part_edges.m (revision 12168) @@ -150,5 +150,5 @@ elemp=md.mesh.elements(irow,:); epartp=epart(irow,:); - nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); + nodeconp=kmlnodeconnectivity(elemp,md.mesh.numberofvertices); [edgeadjp]=edgeadjacency(elemp,nodeconp); [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); Index: /issm/branches/trunk-jpl-damage/src/m/kml/kml_partitions.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/kml_partitions.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/kml/kml_partitions.m (revision 12168) @@ -151,5 +151,5 @@ elemp=md.mesh.elements(irow,:); epartp=epart(irow,:); - nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); + nodeconp=kmlnodeconnectivity(elemp,md.mesh.numberofvertices); [edgeadjp]=edgeadjacency(elemp,nodeconp); [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); Index: /issm/branches/trunk-jpl-damage/src/m/kml/kml_unsh_edges.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/kml_unsh_edges.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/kml/kml_unsh_edges.m (revision 12168) @@ -74,5 +74,5 @@ if (~exist('prtplt','var') || strncmpi(prtplt,'on' ,2) || strncmpi(prtplt,'y',1)) && ... md.qmu.numberofpartitions - [edgeadj]=edgeadjacency(md.mesh.elements,md.nodeconnectivity); + [edgeadj]=edgeadjacency(md.mesh.elements,md.kmlnodeconnectivity); [icol,irow]=find(edgeadj'==0); edgeuns=zeros(length(irow),2); Index: /issm/branches/trunk-jpl-damage/src/m/kml/kmlnodeconnectivity.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/kmlnodeconnectivity.m (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/kml/kmlnodeconnectivity.m (revision 12168) @@ -0,0 +1,58 @@ +% +% create a node connectivity table for the elements in the model. +% +% [nodecon]=edgeadjacency(elem,nnodes,mxepg) +% +% where the required input is: +% elem (numeric, element connectivity array (elems x nodes)) +% +% and the required output is: +% nodecon (numeric, node connectivity array (nnodes x mxepg+1)) +% +% the optional input is: +% nnodes (numeric, number of nodes) +% mxepg (numeric, max elements per node) +% +function [nodecon]=kmlnodeconnectivity(elem,nnodes,mxepg) + +if ~nargin + help kmlnodeconnectivity + return +end + +if ~exist('nnodes','var') || isempty(nnodes) + nnodes=max(max(elem)); +end +if ~exist('mxepg','var') || isempty(mxepg) + mxepg=25; +end + +%% create the node connectivity array + +nodecon=zeros(nnodes,mxepg+1); + +% loop over the elements + +for i=1:size(elem,1) + +% loop over the nodes for each element + + for j=1:size(elem,2) + if elem(i,j) + nodecon(elem(i,j),nodecon(elem(i,j),end)+1)=i; + nodecon(elem(i,j),end)=nodecon(elem(i,j),end)+1; + end + end +end + +%% sort the node connectivity array + +% loop over the nodes + +for i=1:size(nodecon,1) + if (nodecon(i,end) > 1) + nodecon(i,1:nodecon(i,end))=sort(nodecon(i,1:nodecon(i,end))); + end +end + +end Index: sm/branches/trunk-jpl-damage/src/m/kml/nodeconnectivity.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/kml/nodeconnectivity.m (revision 12167) +++ (revision ) @@ -1,58 +1,0 @@ -% -% create a node connectivity table for the elements in the model. -% -% [nodecon]=edgeadjacency(elem,nnodes,mxepg) -% -% where the required input is: -% elem (numeric, element connectivity array (elems x nodes)) -% -% and the required output is: -% nodecon (numeric, node connectivity array (nnodes x mxepg+1)) -% -% the optional input is: -% nnodes (numeric, number of nodes) -% mxepg (numeric, max elements per node) -% -function [nodecon]=nodeconnectivity(elem,nnodes,mxepg) - -if ~nargin - help nodeconnectivity - return -end - -if ~exist('nnodes','var') || isempty(nnodes) - nnodes=max(max(elem)); -end -if ~exist('mxepg','var') || isempty(mxepg) - mxepg=25; -end - -%% create the node connectivity array - -nodecon=zeros(nnodes,mxepg+1); - -% loop over the elements - -for i=1:size(elem,1) - -% loop over the nodes for each element - - for j=1:size(elem,2) - if elem(i,j) - nodecon(elem(i,j),nodecon(elem(i,j),end)+1)=i; - nodecon(elem(i,j),end)=nodecon(elem(i,j),end)+1; - end - end -end - -%% sort the node connectivity array - -% loop over the nodes - -for i=1:size(nodecon,1) - if (nodecon(i,end) > 1) - nodecon(i,1:nodecon(i,end))=sort(nodecon(i,1:nodecon(i,end))); - end -end - -end Index: /issm/branches/trunk-jpl-damage/src/m/model/AnalysisConfiguration.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/AnalysisConfiguration.m (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/model/AnalysisConfiguration.m (revision 12168) @@ -0,0 +1,58 @@ +function [analyses,numanalyses]=AnalysisConfiguration(solutiontype), +%ANALYSISCONFIGURATION - return type of analyses, number of analyses +% +% Usage: +% [analyses, numanalyses]=AnalysisConfiguration(solutiontype); + + + +switch solutiontype, + + case DiagnosticSolutionEnum, + numanalyses=5; + analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum]; + + case SteadystateSolutionEnum, + numanalyses=7; + analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; + + case ThermalSolutionEnum, + numanalyses=2; + analyses=[ThermalAnalysisEnum;MeltingAnalysisEnum]; + + case EnthalpySolutionEnum, + numanalyses=1; + analyses=[EnthalpyAnalysisEnum]; + + case PrognosticSolutionEnum, + numanalyses=1; + analyses=[PrognosticAnalysisEnum]; + + case BalancethicknessSolutionEnum, + numanalyses=1; + analyses=[BalancethicknessAnalysisEnum]; + + case SurfaceSlopeSolutionEnum, + numanalyses=1; + analyses=[SurfaceSlopeAnalysisEnum]; + + case BedSlopeSolutionEnum, + numanalyses=1; + analyses=[BedSlopeAnalysisEnum]; + + case TransientSolutionEnum, + numanalyses=9; + analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum;EnthalpyAnalysisEnum;PrognosticAnalysisEnum]; + + case FlaimSolutionEnum, + numanalyses=1; + analyses=[FlaimAnalysisEnum]; + + case HydrologySolutionEnum, + numanalyses=3; + analyses=[BedSlopeAnalysisEnum;SurfaceSlopeAnalysisEnum;HydrologyAnalysisEnum]; + + otherwise + error('%s%s%s',' solution type: ',EnumToString(solutiontype),' not supported yet!'); + +end Index: /issm/branches/trunk-jpl-damage/src/m/model/MatlabProcessPatch.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/MatlabProcessPatch.m (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/model/MatlabProcessPatch.m (revision 12168) @@ -0,0 +1,65 @@ +function structure=MatlabProcessPatch(structure); +%PROCESSPATCH - create a structure from a patch +% +% Usage: +% Result=ProcessPatch(Result); + +%return if there is no fiel Patch +if (~isfield(structure,'Patch')), + return; +end + +%loop over steps +for i=1:length(structure), + + %Get Patch for current step + Patch=structure(i).Patch; + numvertices=structure(i).PatchVertices; + + %check that Patch is not empty + if length(Patch)==0 continue; end + + %Get number of fields; + fields=unique(Patch(:,1)); + steps=unique(Patch(:,2)); + + %parse steps + for j=1:length(steps), + + posstep=find(Patch(:,2)==steps(j)); + + %Take all the lines of the Patch for this timestep + temporarypatch=Patch(posstep,:); + time=temporarypatch(1,3); + step=temporarypatch(1,2); + + %parse fields + for i=1:length(fields), + + %get name + fieldname=EnumToString(fields(i)); + + %get line positions + pos=find(temporarypatch(:,1)==fields(i)); + + %Fill Result structure + structure(step).steps=step; + structure(step).time=time; + structure(step).(fieldname).element=temporarypatch(pos,4); + structure(step).(fieldname).interpolation=temporarypatch(pos,5); + structure(step).(fieldname).index=temporarypatch(pos,6:5+numvertices); + if structure(step).(fieldname).interpolation==P1Enum, + structure(step).(fieldname).value=temporarypatch(pos,6+numvertices:end); + end + if structure(step).(fieldname).interpolation==P0Enum, + structure(step).(fieldname).value=temporarypatch(pos,6+numvertices); + end + + end + end +end + +%remove fields +structure=rmfield(structure,'Patch'); +structure=rmfield(structure,'PatchVertices'); +structure=rmfield(structure,'PatchNodes'); Index: /issm/branches/trunk-jpl-damage/src/m/model/addnote.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/addnote.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/model/addnote.py (revision 12168) @@ -0,0 +1,29 @@ +def addnote(md, string): + + # Local Variables: md, string, i, notes, miscellaneous, newnotes + # Function calls: ischar, nargout, cell, nargin, length, addnote, error + #ADDNOTE - add a note to the existing model notes field + # + # Usage: + # md=addnote(md,string); + # + # Example: + # md=addnote(md,'Pine Island, Geometry of 2007'); + + if not isinstance(string,basetring): + print 'addnote error message: second input argument should be a string' + return [] + + notes = md.miscellaneous.notes + + if isinstance(notes,basestring): + newnotes=[notes,string] + else: + newnotes=[]; + for i in range(len(notes)): + newnotes=newnotes+notes[i] + + newnotes=newnotes+nodes; + + md.miscellaneous.notes = newnotes + return md Index: /issm/branches/trunk-jpl-damage/src/m/model/collapse.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 12168) @@ -30,6 +30,6 @@ if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end; if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end; -if ~isnan(md.inversion.min_parameters), md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end; -if ~isnan(md.inversion.max_parameters), md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end; +if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end; +if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end; if ~isnan(md.surfaceforcings.mass_balance), md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers); @@ -102,6 +102,6 @@ %lat long -md.mesh.lat=project2d(md,md.mesh.lat,1); -md.mesh.long=project2d(md,md.mesh.long,1); +if numel(md.mesh.lat)>1, md.mesh.lat=project2d(md,md.mesh.lat,1); end +if numel(md.mesh.long)>1, md.mesh.long=project2d(md,md.mesh.long,1); end %Initialize with the 2d mesh Index: sm/branches/trunk-jpl-damage/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/mesh/meshnodensity.m (revision 12167) +++ (revision ) @@ -1,71 +1,0 @@ -function md=meshnodensity(md,domainname,varargin) -%MESH - create model mesh -% -% This routine creates a model mesh using TriMeshNoDensity and a domain outline -% where md is a @model object, domainname is the name of an Argus domain outline file, -% Riftname is an optional argument (Argus domain outline) describing rifts. -% The difference with mesh.m is that the resolution of the mesh follows that of the domain -% outline and the riftoutline -% -% Usage: -% md=meshnodensity(md,domainname) -% or md=meshnodensity(md,domainname,riftname); -% -% Examples: -% md=meshnodensity(md,'DomainOutline.exp'); -% md=meshnodensity(md,'DomainOutline.exp','Rifts.exp'); - -if (nargin==2), - riftname=''; -end -if (nargin==3), - riftname=varargin{1}; -end - -%Mesh using TriMeshNoDensity -if strcmp(riftname,''), - [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); -else - [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname); - - %check that all the created nodes belong to at least one element - orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); - for i=1:length(orphan), - %get rid of the orphan node i - %update x and y - x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; - y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; - %update elements - pos=find(elements>orphan(i)-(i-1)); - elements(pos)=elements(pos)-1; - %update segments - pos1=find(segments(:,1)>orphan(i)-(i-1)); - pos2=find(segments(:,2)>orphan(i)-(i-1)); - segments(pos1,1)=segments(pos1,1)-1; - segments(pos2,2)=segments(pos2,2)-1; - end - - %plug into md - md.mesh.x=x; - md.mesh.y=y; - md.mesh.elements=elements; - md.mesh.segments=segments; - md.mesh.segmentmarkers=segmentmarkers; -end - -%Fill in rest of fields: -md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.mesh.x); -md.mesh.z=zeros(md.mesh.numberofvertices,1); -md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; -md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); -md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); -md.mesh.elementonbed=ones(md.mesh.numberofelements,1); -md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); - -%Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); - -%type of model -md.mesh.dimension=2; Index: sm/branches/trunk-jpl-damage/src/m/model/mesh/meshrefine.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/mesh/meshrefine.m (revision 12167) +++ (revision ) @@ -1,40 +1,0 @@ -function md=meshrefine(md,areas) -%MESHREFINE: refined the mesh from a model, according to an area metric. -% -% Usage: -% md=meshrefine(md,metric) - -%some checks on list of arguments -if ((nargin~=2) | (nargout~=1)), - meshrefineusage(); - error('meshrefine error message'); -end -if ( (isempty(areas)) | (length(areas)~=md.mesh.numberofelements) | (length(find(isnan(areas))))), - meshrefineusage(); - error('meshrefine error message'); -end - -%Refine using TriMeshRefine -[md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes'); - -%Fill in rest of fields: -md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.mesh.x); -md.mesh.z=zeros(md.mesh.numberofvertices,1); -md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; -md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); -md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); -md.mesh.elementonbed=ones(md.mesh.numberofelements,1); -md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); - -%Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); - -%type of model -md.mesh.dimension=2; -end - -function meshrefineusage(), -disp('usage: md=meshrefine(md,areas)'); -end Index: /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.m (revision 12168) @@ -38,33 +38,30 @@ %Mesh using TriMesh -if strcmp(riftname,''), - [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,true); -else - [elements,x,y,segments,segmentmarkers]=TriMeshRifts(domainname,riftname,area,'yes'); +[elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area); - %check that all the created nodes belong to at least one element - orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); - for i=1:length(orphan), - %get rid of the orphan node i - %update x and y - x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; - y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; - %update elements - pos=find(elements>orphan(i)-(i-1)); - elements(pos)=elements(pos)-1; - %update segments - pos1=find(segments(:,1)>orphan(i)-(i-1)); - pos2=find(segments(:,2)>orphan(i)-(i-1)); - segments(pos1,1)=segments(pos1,1)-1; - segments(pos2,2)=segments(pos2,2)-1; - end +%check that all the created nodes belong to at least one element +orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); +for i=1:length(orphan), + disp('WARNING: removing orphans'); + %get rid of the orphan node i + %update x and y + x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; + y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; + %update elements + pos=find(elements>orphan(i)-(i-1)); + elements(pos)=elements(pos)-1; + %update segments + pos1=find(segments(:,1)>orphan(i)-(i-1)); + pos2=find(segments(:,2)>orphan(i)-(i-1)); + segments(pos1,1)=segments(pos1,1)-1; + segments(pos2,2)=segments(pos2,2)-1; +end - %plug into md - md.mesh.x=x; - md.mesh.y=y; - md.mesh.elements=elements; - md.mesh.segments=segments; - md.mesh.segmentmarkers=segmentmarkers; -end +%plug into md +md.mesh.x=x; +md.mesh.y=y; +md.mesh.elements=elements; +md.mesh.segments=segments; +md.mesh.segmentmarkers=segmentmarkers; %Fill in rest of fields: Index: /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/model/mesh/triangle.py (revision 12168) @@ -0,0 +1,56 @@ +from numpy import * +import TriMesh as tm +import NodeConnectivity as nc +import ElementConnectivity as ec + +def triangle(md, domainname, resolution,riftname=''): + #TRIANGLE - create model mesh using the triangle package + # + # This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution + # where md is a @model object, domainname is the name of an Argus domain outline file, + # and resolution is a characteristic length for the mesh (same unit as the domain outline + # unit). Riftname is an optional argument (Argus domain outline) describing rifts. + # + # Usage: + # md=triangle(md,domainname,resolution) + # or md=triangle(md,domainname, resolution, riftname) + # + # Examples: + # md=triangle(md,'DomainOutline.exp',1000); + # md=triangle(md,'DomainOutline.exp',1000,'Rifts.exp'); + + + #Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would + #be made of 1000*1000 area squares). + + #Check that mesh was not already run, and warn user: + if md.mesh.numberofelements != 0.: + choice = input('This model already has a mesh. Are you sure you want to go ahead? (y/n)') + if choice != 'y': + print 'no meshing done ... exiting' + return [] + + area = resolution**2. + + #Mesh using TriMesh + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=tm.TriMesh(domainname,riftname,area) + + + #Fill in rest of fields: + md.mesh.numberofelements = len(md.mesh.elements) + md.mesh.numberofvertices = len(md.mesh.x) + md.mesh.z = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1] = 1. + md.mesh.vertexonbed = ones(md.mesh.numberofvertices) + md.mesh.vertexonsurface = ones(md.mesh.numberofvertices) + md.mesh.elementonbed = ones(md.mesh.numberofelements) + md.mesh.elementonsurface = ones(md.mesh.numberofelements) + + #Now, build the connectivity tables for this mesh. + [md.mesh.vertexconnectivity]= nc.NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) + [md.mesh.elementconnectivity] = ec.ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity) + + #type of model + md.mesh.dimension = 2. + return md Index: /issm/branches/trunk-jpl-damage/src/m/model/modis.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/modis.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/modis.m (revision 12168) @@ -14,9 +14,9 @@ %Get path to gdal binaries -path_gdal=[issmtier() '/externalpackages/gdal/install/bin/']; +path_gdal=[issmdir() '/externalpackages/gdal/install/bin/']; %Was gdal compiled? if ~exist([path_gdal 'gdal_translate']), - error(['modis error message: GDAL library needs to be compiled to use this routine. Compile GDAL in ' issmtier() '/externalpackages/gdal to use this routine.']); + error(['modis error message: GDAL library needs to be compiled to use this routine. Compile GDAL in ' issmdir() '/externalpackages/gdal to use this routine.']); end Index: /issm/branches/trunk-jpl-damage/src/m/model/parameterization/parameterize.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/parameterization/parameterize.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/model/parameterization/parameterize.py (revision 12168) @@ -0,0 +1,27 @@ +import os +def parameterize(md,parametername): + #PARAMETERIZE - parameterize a model + # + # from a parameter matlab file, start filling in all the model fields that were not + # filled in by the mesh.py and setmask.py model methods. + # Warning: the parameter file must be able to be run in Python + # + # Usage: + # md=parameterize(md,parametername) + # + # Example: + # md=parameterize(md,'Square.par'); + + #some checks + if not os.path.isfile(parametername): + print 'parameterize error message: file '+parametername+' not found.' + return [] + + #Try and run parameter file. + execfile(parametername) + + #ame and notes + if len(md.miscellaneous.name)==0: + md.miscellaneous.name=os.path.basename(parametername) + + md=addnote(md,'Model created by using parameter file: '+parametername+' on: '+str(datetime.datetime.now())) Index: /issm/branches/trunk-jpl-damage/src/m/model/petscversion.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/petscversion.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/petscversion.m (revision 12168) @@ -8,5 +8,5 @@ PETSC_VERSION=3; -configfile=[issmtier() '/config.h']; +configfile=[issmdir() '/config.h']; if ~exist(configfile,'file'), error(['File ' configfile ' not found. ISSM has not been configured yet!']); Index: /issm/branches/trunk-jpl-damage/src/m/model/plot/applyoptions.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/plot/applyoptions.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/plot/applyoptions.m (revision 12168) @@ -229,4 +229,7 @@ warning on MATLAB:log:logOfZero; set(c,'YTickLabel',labels); + end + if exist(options,'cbYLim'); + set(c,'YLim',getfieldvalue(options,'cbYLim')); end if exist(options,'colorbartitle'), Index: /issm/branches/trunk-jpl-damage/src/m/model/plot/northarrow.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/plot/northarrow.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/plot/northarrow.m (revision 12168) @@ -72,5 +72,5 @@ %Text North -xN=max([A(1) D(1) E(1) F(1) G(1)])+ratio/3*lengtharrow; +xN=max([A(1) D(1) E(1) F(1) G(1)])+ratio/3*abs(lengtharrow); yN=mean([A(2) F(2) H(2)]); text(xN,yN,'North','FontSize',fontsize,'FontWeight','b'); Index: /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_gridded.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_gridded.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_gridded.m (revision 12168) @@ -40,4 +40,5 @@ data_max=max(data_grid(:)); end +options=changefieldvalue(options,'cbYLim',[data_min data_max]); if whitepos==1, white =data_max + (data_max-data_min)/55; Index: /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_overlay.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_overlay.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/model/plot/plot_overlay.m (revision 12168) @@ -96,5 +96,5 @@ %h_data(find(data_grid>data_mean))=1; h_data=1*ones(size(data_grid)); - h_data(find(data_grid>data_mean))=0.7; + h_data(find(data_gridxlim(1) & md.mesh.yylim(1)); + flag=prod(flag_nodes(md.mesh.elements),2); + else: + #ok, flag elements + flag=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x,md.mesh.y,region,'element',1); + + if invert: + flag=~flag; + + elif isinstance(region,nparray): + if len(region)!=md.mesh.numberofelements: + print FlagElements.__doc__ + print 'Flaglist for region must be of same size as number of elements in model' + return [] + flag=region; + else: + print 'Invalid region option' + return [] + + return flag; Index: sm/branches/trunk-jpl-damage/src/m/utils/ImageProcessing/gradient_perso.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/ImageProcessing/gradient_perso.m (revision 12167) +++ (revision ) @@ -1,91 +1,0 @@ -function [ax,ay ]=gradient_perso(a,dx,dy,n); -%GRADIENT_PERSO - gradient computation -% -% INPUT a,dx,dy,n where a is the scalar value, dx and dy the spacing of one pixel -% in a and n is the width wanted in the gradient computation, in pixels. -% -% Usage: -% [ax,ay ]=gradient_perso(a,dx,dy,n) - -s=size(a); -ax=zeros(s(1),s(2)); -ay=zeros(s(1),s(2)); - -for k=n+1:s(1)-n, - if mod(k,10)==0, - disp(k/s(1)*100); - end - - for j=n+1:s(2)-n, - if isnan(a(k,j)), - ax(k,j)=NaN; - ay(k,j)=NaN; - else - temp=a(k,j); - temp2=a(k,j); - - count=1; - while ~isnan(a(k,j+count)), - temp=[temp a(k,j+count)]; - count=count+1; - if count>n, - count=count-1; - break; - end - - end - count=1; - while ~isnan(a(k,j-count)), - temp=[a(k,j-count) temp]; - count=count+1; - if count>n, - count=count-1; - break; - end - - end - - count=1; - while ~isnan(a(k+count,j)), - temp2=[temp2 a(k+count,j)]; - count=count+1; - if count>n, - count=count-1; - break; - end - - end - count=1; - while ~isnan(a(k-count,j)), - temp2=[a(k-count,j) temp2]; - count=count+1; - if count>n, - count=count-1; - break; - end - - end - - if length(temp)==1, - ax(k,j)=NaN; - else - ax(k,j)=(temp(length(temp))-temp(1))/(length(temp)-1)/dx; - end - - if length(temp2)==1, - ay(k,j)=NaN; - else - ay(k,j)=(temp2(length(temp2))-temp2(1))/(length(temp2)-1)/dy; - end - - end - end -end - - - - - - - - Index: sm/branches/trunk-jpl-damage/src/m/utils/ImageProcessing/transp.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/ImageProcessing/transp.m (revision 12167) +++ (revision ) @@ -1,10 +1,0 @@ -bg = uint8(255.*rand(100, 100, 3)); -imview(bg); - -fg(:, :, 1) = uint8(255 .*(cumsum(ones(100, 100)) ./ 100));% -fg(:, :, 2) = uint8(zeros(100)); -fg(:, :, 3) = flipud(fg(:, :, 1)); -imview(fg); - -res=immerge(bg, fg, .3); -imview(res); Index: /issm/branches/trunk-jpl-damage/src/m/utils/Meca/paterson.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Meca/paterson.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Meca/paterson.py (revision 12168) @@ -0,0 +1,50 @@ +from numpy import * + +def paterson(temperature): + + # Local Variables: pos11, pos5, pos10, temperature, pos, T, pos8, pos9, pos6, pos7, pos4, rigidity, pos2, pos3, pos1 + # Function calls: length, zeros, argwhere, paterson, error + #PATERSON - figure out the rigidity of ice for a given temperature + # + # rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). + # temperature is in Kelvin degrees + # + # Usage: + # rigidity=paterson(temperature) + + pos=argwhere(temperature<0.) + if len(pos): + print 'input temperature should be in Kelvin (positive)' + return [] + + T = temperature-273.15 + #The routine below is equivalent to: + # n=3; T=temperature-273; + # %From paterson, + # Temp=[0;-2;-5;-10;-15;-20;-25;-30;-35;-40;-45;-50]; + # A=[6.8*10^-15;2.4*10^-15;1.6*10^-15;4.9*10^-16;2.9*10^-16;1.7*10^-16;9.4* + # 10^-17;5.1*10^-17;2.7*10^-17;1.4*10^-17;7.3*10^-18;3.6*10^-18];;%s-1(kPa-3) + # %Convert into rigidity B + # B=A.^(-1/n)*10^3; %s^(1/3)Pa + # %Now, do a cubic fit between Temp and B: + # fittedmodel=fit(Temp,B,'cubicspline'); + # rigidity=fittedmodel(temperature); + + rigidity=zeros(len(T)) + pos1=argwhere(T<=-45); rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) + pos2=argwhere(logical_and(-45<=T,T<-40)); rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) + pos3=argwhere(logical_and(-40<=T,T<-35)); rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) + pos4=argwhere(logical_and(-35<=T,T<-30)); rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) + pos5=argwhere(logical_and(-30<=T,T<-25)); rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) + pos6=argwhere(logical_and(-25<=T,T<-20)); rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) + pos7=argwhere(logical_and(-20<=T,T<-15)); rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) + pos8=argwhere(logical_and(-15<=T,T<-10)); rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) + pos9=argwhere(logical_and(-10<=T,T<-5)); rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) + pos10=argwhere(logical_and(-5<=T,T<-2)); rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) + pos11=argwhere(-2<=T); rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) + + #Now make sure that rigidity is positive + pos=argwhere(rigidity<0); rigidity[pos]=1**6 + + return rigidity + Index: /issm/branches/trunk-jpl-damage/src/m/utils/Miscellaneous/issmdoc.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Miscellaneous/issmdoc.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Miscellaneous/issmdoc.m (revision 12168) @@ -2,9 +2,9 @@ %First get ISSM tier: -ISSM_TIER=issmtier; +ISSM_DIR=issmdir; disp(sprintf('\n%s',' A comprehensive documentation is available on http://issm.jpl.nasa.gov')); disp(sprintf('\n%s',' Example: how to create a square ice shelf')); -disp(sprintf('%s',' go to ',ISSM_TIER,'/examples/SquareIceshelf')); +disp(sprintf('%s',' go to ',ISSM_DIR,'/examples/SquareIceshelf')); disp(sprintf('%s',' md=model; %creates a new empty model structure')); disp(sprintf('%s',' md=triangle(md,''DomainOutline.exp'',50000); %creates a mesh of the domain outline with a resolution of 50000m')); Index: /issm/branches/trunk-jpl-damage/src/m/utils/OS/ispetsc.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/OS/ispetsc.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/OS/ispetsc.m (revision 12168) @@ -6,5 +6,5 @@ -configfile=[issmtier() '/bin/config.h']; %should find it in the install target +configfile=[issmdir() '/bin/config.h']; %should find it in the install target if ~exist(configfile,'file'), error(['File ' configfile ' not found. ISSM has not been configured yet!']); Index: /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpin.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpin.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpin.m (revision 12168) @@ -32,10 +32,10 @@ %use the putty project pscp.exe: it should be in the path. - %get ISSM_TIER variable - [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); if status, - error('scpin error message: could not find ISSM_TIER_WIN envirnoment variable'); + error('scpin error message: could not find ISSM_DIR_WIN envirnoment variable'); end - ISSM_TIER=ISSM_TIER(2:end-2); + ISSM_DIR=ISSM_DIR(2:end-2); username=input('Username: (quoted string) '); @@ -43,5 +43,5 @@ for i=1:numel(packages), - [status,result]=system([ISSM_TIER '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']); + [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']); if status, error('scpin error message: could not call putty pscp'); Index: /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpout.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpout.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmscpout.m (revision 12168) @@ -23,10 +23,10 @@ %use the putty project pscp.exe: it should be in the path. - %get ISSM_TIER variable - [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); if status, - error('scpout error message: could not find ISSM_TIER_WIN envirnoment variable'); + error('scpout error message: could not find ISSM_DIR_WIN envirnoment variable'); end - ISSM_TIER=ISSM_TIER(2:end-2); + ISSM_DIR=ISSM_DIR(2:end-2); username=input('Username: (quoted string) '); @@ -34,5 +34,5 @@ for i=1:numel(packages), - [status,result]=system([ISSM_TIER '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]); + [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]); if status, error('scpout error message: could not call putty pscp'); Index: /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmssh.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmssh.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/OS/issmssh.m (revision 12168) @@ -15,15 +15,15 @@ %use the putty project plink.exe: it should be in the path. - %get ISSM_TIER variable - [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); if status, - error('issmssh error message: could not find ISSM_TIER_WIN envirnoment variable'); + error('issmssh error message: could not find ISSM_DIR_WIN envirnoment variable'); end - ISSM_TIER=ISSM_TIER(2:end-2); + ISSM_DIR=ISSM_DIR(2:end-2); username=input('Username: (quoted string) '); key=input('Key: (quoted string) '); - system([ISSM_TIER '/externalpackages/ssh/plink.exe -ssh -l "' username '" -pw "' key '" ' host ' "' command '"']); + system([ISSM_DIR '/externalpackages/ssh/plink.exe -ssh -l "' username '" -pw "' key '" ' host ' "' command '"']); else Index: /issm/branches/trunk-jpl-damage/src/m/utils/Shell/flaimdir.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Shell/flaimdir.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Shell/flaimdir.m (revision 12168) @@ -5,3 +5,3 @@ % FLAIM_DIR=flaimdir() -FLAIM_DIR=[issmtier '/externalpackages/flaim/install']; +FLAIM_DIR=[issmdir '/externalpackages/flaim/install']; Index: /issm/branches/trunk-jpl-damage/src/m/utils/Shell/issmdir.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Shell/issmdir.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Shell/issmdir.m (revision 12168) @@ -1,4 +1,4 @@ function ISSM_DIR=issmdir() -%ISSMDIR - Get ISSM_DIR environment variable contents. +%ISSMDIR - Get ISSM_DIR environment variable % % Usage: @@ -9,4 +9,7 @@ else ISSM_DIR =getenv('ISSM_DIR_WIN'); + if strcmpi(ISSM_DIR(end),'/') | strcmpi(ISSM_DIR(end),'\'), + ISSM_DIR = ISSM_DIR(1:end-1); %shave off the last '/' + end end Index: sm/branches/trunk-jpl-damage/src/m/utils/Shell/issmtier.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Shell/issmtier.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -function ISSM_TIER=issmtier() -%ISSMTIER - Get ISSM_TIER environment variable contents. -% -% Usage: -% ISSM_TIER=issmtier() - -if ~ispc, - ISSM_TIER =getenv('ISSM_TIER'); -else - ISSM_TIER =getenv('ISSM_TIER_WIN'); - if strcmpi(ISSM_TIER(end),'/') | strcmpi(ISSM_TIER(end),'\'), - ISSM_TIER = ISSM_TIER(1:end-1); %shave off the last '/' - end -end - -if (isempty(ISSM_TIER)), - error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); -end Index: /issm/branches/trunk-jpl-damage/src/m/utils/Shell/jplsvn.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Shell/jplsvn.m (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Shell/jplsvn.m (revision 12168) @@ -0,0 +1,15 @@ +function JPL_SVN=jplsvn() +%ISSMDIR - Get JPL_SVN environment variable +% +% Usage: +% JPL_SVN=jplsvn() + +if ~ispc, + JPL_SVN =getenv('JPL_SVN'); +else + JPL_SVN =getenv('JPL_SVN_WIN'); +end + +if (isempty(JPL_SVN)), + error('jplsvn error message: ''JPL_SVN'' environment variable is empty! You should define JPL_SVN in your .cshrc or .bashrc'); +end Index: /issm/branches/trunk-jpl-damage/src/m/utils/Shell/ucisvn.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Shell/ucisvn.m (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Shell/ucisvn.m (revision 12168) @@ -0,0 +1,15 @@ +function UCI_SVN=ucisvn() +%ISSMDIR - Get UCI_SVN environment variable +% +% Usage: +% UCI_SVN=ucisvn() + +if ~ispc, + UCI_SVN =getenv('UCI_SVN'); +else + UCI_SVN =getenv('UCI_SVN_WIN'); +end + +if (isempty(UCI_SVN)), + error('ucisvn error message: ''UCI_SVN'' environment variable is empty! You should define UCI_SVN in your .cshrc or .bashrc'); +end Index: /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.cpp (revision 12168) @@ -0,0 +1,62 @@ +/*!\file: AverageFilter.cpp + * \brief fill holes in matlab velocity array + this matlab module is an adaptation of a routine written by Robber + Crippen. The original routine was designed for the SRTM mission at JPL, + and can be found in the current directory, under the name + AverageFilterCrippen. It fills void holes in an image, using an interpolation + algorithm, and optionnally a smoothing algorithm. + This matlab module extends the Crippen routine to be used in Matlab, + using double arrays found in the workspace, and loaded directly into memory. +*/ + + +#include "./AverageFilter.h" + +void mexFunction( int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + int i,j; + + /* required input: */ + double* imagein=NULL; + int imagein_rows,imagein_cols; + int smooth; + + + /* output: */ + mxArray* pfield=NULL; + double* imageout=NULL; + int imageout_rows,imageout_cols; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&AverageFilterUsage); + + /*Fetch data: */ + FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN); + FetchData(&smooth,SMOOTH); + + /*Run core hole filler routine: */ + AverageFilterx( &imageout,imagein,imagein_rows,imagein_cols,smooth); + + /* output: */ + WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols); + + /*end module: */ + MODULEEND(); +} + + +void AverageFilterUsage(void) +{ + printf(" AverageFilter usage:\n"); + printf(" [image_out]=AverageFilter(image_in,pixels);\n\n"); + printf(" where:\n"); + printf(" image_in in double format\n"); + printf(" pixels: characteristic size of smoothing\n"); + printf(" image_out in double format\n"); + printf("\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/AverageFilter/AverageFilter.h (revision 12168) @@ -0,0 +1,36 @@ + +/* + AverageFilter.h +*/ + + +#ifndef _AVERAGEFILTER_H +#define _AVERAGEFILTER_H + +/* local prototypes: */ +void AverageFilterUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "AverageFilter" + + +/* serial input macros: */ +#define IMAGEIN prhs[0] +#define SMOOTH prhs[1] + +/* serial output macros: */ +#define IMAGEOUT &plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 2 + +#endif /* _AVERAGEFILTER_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 12168) @@ -0,0 +1,86 @@ +/*\file BamgConvertMesh.c + *\brief: bamg module. + */ +#include "./BamgConvertMesh.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input: */ + double* index=NULL; + int index_rows; + double* x=NULL; + int x_cols; + double* y=NULL; + int y_rows; + int y_cols; + + /*Output*/ + BamgMesh* bamgmesh=NULL; + BamgGeom* bamggeom=NULL; + mxArray* bamgmesh_mat=NULL; + mxArray* bamggeom_mat=NULL; + + /*Intermediary*/ + int nods; + int nels; + int verbose=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgConvertMeshUsage); + + /*Initialize Bamg outputs*/ + bamggeom=new BamgGeom(); + bamgmesh=new BamgMesh(); + + /*Input datasets: */ + if (verbose) printf("Fetching inputs\n"); + FetchData(&index,&nels,&index_rows,INDEXHANDLE); + FetchData(&x,&nods,&x_cols,XHANDLE); + FetchData(&y,&y_rows,&y_cols,YHANDLE); + + /*Check inputs*/ + if (nels<0){ + _error_("Number of elements must be positive, check index number of lines"); + } + if (nods<0){ + _error_("Number of nods must be positive, check x and y sizes"); + } + if (index_rows!=3){ + _error_("index should have 3 columns"); + } + if (y_rows!=nods){ + _error_("x and y do not have the same length"); + } + if (x_cols>1 || y_cols>1){ + _error_("x and y should have only one column"); + } + + /* Run core computations: */ + if (verbose) printf("Call core\n"); + BamgConvertMeshx(bamgmesh,bamggeom,index,x,y,nods,nels); + + /*Generate output Matlab Structures*/ + WriteData(BAMGGEOMOUT,bamggeom); + WriteData(BAMGMESHOUT,bamgmesh); + + /*Clean up*/ + delete bamggeom; + delete bamgmesh; + + /*end module: */ + MODULEEND(); +} + +void BamgConvertMeshUsage(void) +{ + _printf_(true,"BAMGCONVERTMESH - convert [x y index] to a bamg geom and mesh geom"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [bamggeom bamgmesh]=BamgConvertMesh(index,x,y);\n"); + _printf_(true," index: index of the mesh\n"); + _printf_(true," x,y: coordinates of the nodes\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgConvertMesh/BamgConvertMesh.h (revision 12168) @@ -0,0 +1,36 @@ +/*!\file BamgConvertMesh.h + * \brief: prototype for Data Interpolation mex module. + */ + +#ifndef _BAMGCONVERTMESH_H +#define _BAMGCONVERTMESH_H + +/* local prototypes: */ +void BamgConvertMeshUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "BamgConvertMesh" + + +/* serial input macros: */ +#define INDEXHANDLE prhs[0] +#define XHANDLE prhs[1] +#define YHANDLE prhs[2] + +/* serial output macros: */ +#define BAMGMESHOUT (mxArray**)&plhs[0] +#define BAMGGEOMOUT (mxArray**)&plhs[1] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 2 +#undef NRHS +#define NRHS 3 + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.cpp (revision 12168) @@ -0,0 +1,56 @@ +/*\file BamgMesher.c + *\brief: mesher that uses the bamg library + */ +#include "./BamgMesher.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*Outputs*/ + mxArray* bamgmesh_mat=NULL; + mxArray* bamggeom_mat=NULL; + + /*diverse: */ + BamgOpts *bamgopts=NULL; + BamgMesh *bamgmesh_in=NULL; + BamgGeom *bamggeom_in=NULL; + BamgMesh *bamgmesh_out=NULL; + BamgGeom *bamggeom_out=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgMesherUsage); + + /*Initialize outputs*/ + bamggeom_out=new BamgGeom(); + bamgmesh_out=new BamgMesh(); + + /*Fetch inputs: */ + FetchData(&bamgopts,BAMGOPTIONS); + FetchData(&bamggeom_in,BAMGGEOMIN); + FetchData(&bamgmesh_in,BAMGMESHIN); + + /*Call x layer*/ + Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); + + /*Generate output Matlab Structures*/ + WriteData(BAMGGEOMOUT,bamggeom_out); + WriteData(BAMGMESHOUT,bamgmesh_out); + + /*Free ressources: */ + delete bamgopts; + delete bamggeom_in; + delete bamggeom_out; + delete bamgmesh_in; + delete bamgmesh_out; + + /*end module: */ + MODULEEND(); +} + +void BamgMesherUsage(void){ + _printf_(true,"\n"); + _printf_(true," usage: [bamgmesh,bamggeom]=%s(bamgmesh,bamggeom,bamgoptions);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgMesher/BamgMesher.h (revision 12168) @@ -0,0 +1,36 @@ +/* + BamgMesherUsage.h +*/ + +#ifndef _BAMG_MESHER_H_ +#define _BAMG_MESHER_H_ + +/* local prototypes: */ +void BamgMesherUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "BamgMesher" + +/* serial input macros: */ +#define BAMGMESHIN (mxArray*)prhs[0] +#define BAMGGEOMIN (mxArray*)prhs[1] +#define BAMGOPTIONS (mxArray*)prhs[2] + +/* serial output macros: */ +#define BAMGMESHOUT (mxArray**)&plhs[0] +#define BAMGGEOMOUT (mxArray**)&plhs[1] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 2 +#undef NRHS +#define NRHS 3 + +#endif /* _BAMG_MESHER_H_ */ + Index: /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.cpp (revision 12168) @@ -0,0 +1,58 @@ +/*\file BamgTriangulate.c + *\brief: bamg module. + */ +#include "./BamgTriangulate.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input: */ + double* x=NULL; + double* y=NULL; + int x_cols; + int y_rows,y_cols; + int nods; + + /*Output*/ + int* index=NULL; + int nels; + + /*Intermediary*/ + int verbose=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgTriangulateUsage); + + /*Input datasets: */ + if (verbose) printf("Fetching inputs\n"); + FetchData(&x,&nods,&x_cols,XHANDLE); + FetchData(&y,&y_rows,&y_cols,YHANDLE); + + /*Check inputs*/ + if(y_rows!=nods) _error_("x and y do not have the same length"); + if(x_cols>1 || y_cols>1) _error_("x and y should have only one column"); + if(nods<3) _error_("At least 3 points are required"); + + /* Run core computations: */ + if (verbose) printf("Call core\n"); + BamgTriangulatex(&index,&nels,x,y,nods); + + /*Write output*/ + WriteData(INDEX,index,nels,3); + + /*end module: */ + MODULEEND(); +} + +void BamgTriangulateUsage(void) +{ + _printf_(true,"BAMGTRIANGULATE - Delaunay Triangulation of a list of points"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," index=BamgTriangulate(x,y);\n"); + _printf_(true," index: index of the triangulation\n"); + _printf_(true," x,y: coordinates of the nodes\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/BamgTriangulate/BamgTriangulate.h (revision 12168) @@ -0,0 +1,34 @@ +/*!\file BamgTriangulate.h + * \brief: prototype for Data Interpolation mex module. + */ + +#ifndef _BAMGTRIANGULATE_H +#define _BAMGTRIANGULATE_H + +/* local prototypes: */ +void BamgTriangulateUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "BamgTriangulate" + + +/* serial input macros: */ +#define XHANDLE prhs[0] +#define YHANDLE prhs[1] + +/* serial output macros: */ +#define INDEX (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 2 + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/Chaco/Chaco.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Chaco/Chaco.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Chaco/Chaco.cpp (revision 12168) @@ -0,0 +1,137 @@ +/*\file Chaco.c + *\brief: Chaco partitioner mex module + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "./Chaco.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i; + int nterms; + + /*Inputs: */ + int nvtxs; /* number of vertices in graph */ + int *start; /* start of edge list for each vertex */ + int *adjacency; /* edge list data */ + int *vwgts = NULL; /* weights for all vertices */ + int nedges; + float *ewgts = NULL; /* weights for all edges */ + float *x = NULL; + float *y = NULL; + float *z = NULL; /* coordinates for inertial method */ + double options[10] = {1,1,0,0,1,1,50,0,.001,7654321}; /* architecture and partitioning options */ + double *in_options = NULL; + int *nparts = NULL; /* number of parts options */ + int npart; + double *goal = NULL; /* desired set sizes */ + + /*intermediary pointers: */ + mwIndex *mwstart, *mwadjacency; + double *doublepointer; + + /*output: */ + short *assignment = NULL; /* set number of each vtx (length nvtxs+1) */ + double *doubleassignment = NULL; /*holds assignment, in double format, to return to matlab */ + + #ifndef _HAVE_CHACO_ //only works if dakota library has been compiled in. + _error_(" Chaco not available! Cannot carry out Chaco partitioning!"); + #endif + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ChacoUsage); + + /*Fetch adjacency matrix: */ + nvtxs = mxGetN(A_IN); + mwstart = mxGetJc(A_IN); + start=(int*)xmalloc((nvtxs+1)*sizeof(int)); + for (i=0; i +#include /* strcasecmp */ +#include /* clock,time,difftime */ + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +/* serial input macros: */ +#define A_IN (mxArray*)prhs[0] +#define VWGTS_IN (mxArray*)prhs[1] +#define EWGTS_IN (mxArray*)prhs[2] +#define X_IN (mxArray*)prhs[3] +#define Y_IN (mxArray*)prhs[4] +#define Z_IN (mxArray*)prhs[5] +#define OPTNS_IN (mxArray*)prhs[6] +#define NPARTS_IN (mxArray*)prhs[7] +#define GOAL_IN (mxArray*)prhs[8] + +/* serial output macros: */ +#define ASSGN_OUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 9 + +#undef __FUNCT__ +#define __FUNCT__ "Chaco" + +#endif /* _CHACO_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12168) @@ -0,0 +1,113 @@ +/*! \file ContourtoMesh + \brief: takes an contour file, and figures out which nodes or elements from the mesh + are inside this contour. + usage: + [in_nod,in_elem]=ContourToMesh(index,x,y,contours,interptype,edgevalue); + + input: + + index,x,y: delaunay triangulation. + contours: structure holding sets of vertices making open contours. + interptype: string definining type of interpolation ('element', or 'node', or 'element and node'); + edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons + + output: + in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', + or of size 0 otherwise. + in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', + or of size 0 otherwise. +*/ + +#include "./ContourToMesh.h" + +WRAPPER(ContourToMesh){ + + int i,j; + + /* required input: */ + int edgevalue; + double *index = NULL; + int nel; + double *x = NULL; + int nods; + double *y = NULL; + char *interptype = NULL; + char* contourname = NULL; + DataSet* contours = NULL; + + /* output: */ + Vector *in_nod = NULL; + Vector *in_elem = NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on output arguments on the matlab side: */ + #ifdef _HAVE_MATLAB_MODULES_ + if(nlhs!=1 && nlhs!=2){ + ContourToMeshUsage(); + _error_(" usage. See above"); + } + #endif + /*check on input arguments: */ + if(nrhs!=NRHS){ + ContourToMeshUsage(); + _error_(" usage. See above"); + } + + + /*Fetch inputs: */ + FetchData(&index,&nel,NULL,INDEX); + FetchData(&x,&nods,NULL,X); + FetchData(&y,NULL,NULL,Y); + FetchData(&edgevalue,EDGEVALUE); + FetchData(&contourname,CONTOURNAME); + contours=DomainOutlineRead(contourname); + + /*Fetch interptype: */ + FetchData(&interptype,INTERPTYPE); + + /*Run interpolation routine: */ + ContourToMeshx( &in_nod,&in_elem,index,x,y,contours,interptype,nel,nods,edgevalue); + + /* output: */ + if (strcmp(interptype,"node")==0){ + WriteData(PLHS0,in_nod); + } + else if (strcmp(interptype,"element")==0){ + WriteData(PLHS0,in_elem); + } + else if (strcmp(interptype,"element and node")==0){ + WriteData(PLHS0,in_nod); + WriteData(PLHS1,in_elem); + } + else _error_(" wrong interpolation type"); + + /*end module: */ + MODULEEND(); + +} + +void ContourToMeshUsage(void)//{{{1 +{ + printf("CONTOURTOMESH - Flag the elements or nodes inside a contour\n"); + printf("\n"); + printf(" Usage: \n"); + printf(" [in_nod,in_elem]=ContourToMesh(index,x,y,contourname,interptype,edgevalue)\n\n"); + printf("\n"); + printf(" index,x,y: mesh triangulation.\n"); + printf(" contourname: name of .exp file containing the contours.\n"); + printf(" interptype: string definining type of interpolation ('element', or 'node').\n"); + printf(" edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n"); + printf(" in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', \n"); + printf(" or of size 0 otherwise.\n"); + printf(" in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', \n"); + printf(" or of size 0 otherwise.\n"); + printf("\n"); + printf(" Example: \n"); + printf(" in_nod=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','node',1)\n"); + printf(" in_elements=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element',0)\n"); + printf(" [in_nodes,in_elements]=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element and node',0)\n"); + printf("\n"); +} +//}}} Index: /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ContourToMesh/ContourToMesh.h (revision 12168) @@ -0,0 +1,72 @@ + +/* + ContourToMesh.h +*/ + + +#ifndef _CONTOURTOMESH_H +#define _CONTOURTOMESH_H + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +/*Header files: */ +#include "../../c/include/globals.h" +#include "../../c/toolkits/toolkits.h" +#include "../../c/include/include.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" +#include "../../c/io/io.h" +#include "../../c/EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define INDEX (mxArray *)prhs[0] +#define X (mxArray *)prhs[1] +#define Y (mxArray *)prhs[2] +#define CONTOURNAME (mxArray *)prhs[3] +#define INTERPTYPE (mxArray *)prhs[4] +#define EDGEVALUE (mxArray *)prhs[5] +/* serial output macros: */ +#define PLHS0 (mxArray**)&plhs[0] +#define PLHS1 (mxArray**)&plhs[1] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define INDEX PyTuple_GetItem(args,0) +#define X PyTuple_GetItem(args,1) +#define Y PyTuple_GetItem(args,2) +#define CONTOURNAME PyTuple_GetItem(args,3) +#define INTERPTYPE PyTuple_GetItem(args,4) +#define EDGEVALUE PyTuple_GetItem(args,5) +/* serial output macros: */ +#define PLHS0 output,0 +#define PLHS1 output,1 +#endif + +#undef __FUNCT__ +#define __FUNCT__ "ContourToMesh" + +/* serial arg counts: */ +#undef NLHS +#define NLHS 2 +#undef NRHS +#define NRHS 6 + +/* local prototypes: */ +void ContourToMeshUsage(void); + +#endif /* _CONTOURTOMESH_H */ + Index: /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.cpp (revision 12168) @@ -0,0 +1,114 @@ +/*! \file ContourtoNodes + \brief: takes a contour file, and figures out which nodes (x,y list) + are inside this contour. + + usage: + [flags]=ContourToNodes(x,y,contours,interptype,edgevalue); + + where: + + input: + + x,y: node cooredinates + + contours: structure holding sets of vertices making open contours. + + interptype: string definining type of interpolation ('element', or 'node', or 'element and node'); + + edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons + + output: + flags: vector of flags (0 or 1), of size nods +*/ + +#include "./ContourToNodes.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + + int i,j; + + /* required input: */ + double* x=NULL; + double* y=NULL; + int edgevalue; + char* interptype=NULL; + + /* output: */ + Vector* flags=NULL; + int nods; + + //contours + mxArray* matlabstructure=NULL; + int numcontours; + Contour** contours=NULL; + Contour* contouri=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ContourToNodesUsage); + + + /*Fetch inputs: */ + FetchData(&x,&nods,NULL,XHANDLE); + FetchData(&y,NULL,NULL,YHANDLE); + FetchData(&edgevalue,EDGEVALUEHANDLE); + + //Fetch contours + + if(mxIsChar(FILENAME)){ + /*Call expread on filename to build a contour array in the matlab workspace: */ + mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); + } + else{ + /*FILENAME is actually a structure, coming directly from expread: */ + matlabstructure=(mxArray*)FILENAME; + } + + numcontours=mxGetNumberOfElements(matlabstructure); + contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. + contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); + contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); + *(contours+i)=contouri; + } + + /* Debugging of contours :{{{1*/ + /*for(i=0;inods); + for (j=0;jnods;j++){ + printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); + } + }*/ + /*}}}*/ + + /*Run interpolation routine: */ + ContourToNodesx(&flags,x,y,nods,contours,numcontours,edgevalue); + + /* output: */ + WriteData(FLAGS,flags); + + /*end module: */ + MODULEEND(); + +} + +void ContourToNodesUsage(void){ + printf(" usage:\n"); + printf(" [flags]=ContourToNodes(x,y,contourname,edgevalue);\n\n"); + printf(" where:\n"); + printf(" x,y: list of nodes.\n"); + printf(" contourname: name of .exp file containing the contours, or resulting structure from call to expread.\n"); + printf(" interptype: string definining type of interpolation ('element', or 'node').\n"); + printf(" edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n"); + printf(" flags: vector of flags (0 or 1), of size nods.\n"); + printf("\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ContourToNodes/ContourToNodes.h (revision 12168) @@ -0,0 +1,44 @@ + +/* + ContourToNodes.h +*/ + + +#ifndef _CONTOURTONODES_H +#define _CONTOURTONODES_H + +/* local prototypes: */ +void ContourToNodesUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "ContourToNodes" + + +#ifndef ALL +#define ALL 0 +#endif + +/* input macros: */ +#define XHANDLE prhs[0] +#define YHANDLE prhs[1] +#define FILENAME prhs[2] +#define EDGEVALUEHANDLE prhs[3] + +/* serial output macros: */ +#define FLAGS (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 4 + + +#endif /* _CONTOURTONODES_H */ + Index: /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 12168) @@ -0,0 +1,42 @@ +/*\file ElementConnectivity.c + *\brief: build element connectivity using node connectivity and elements. + */ + +#include "./ElementConnectivity.h" + +WRAPPER(ElementConnectivity){ + + /*inputs: */ + double* elements=NULL; + double* nodeconnectivity=NULL; + int nel,nods; + int width; + + /*outputs: */ + double* elementconnectivity=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments: */ + CHECKARGUMENTS(NLHS,NRHS,&ElementConnectivityUsage); + + /*Input datasets: */ + FetchData(&elements,&nel,NULL,ELEMENTS); + FetchData(&nodeconnectivity,&nods,&width,NODECONNECTIVITY); + + /*!Generate internal degree of freedom numbers: */ + ElementConnectivityx(&elementconnectivity, elements,nel, nodeconnectivity, nods, width); + + /*write output datasets: */ + WriteData(ELEMENTCONNECTIVITY,elementconnectivity,nel,3); + + /*end module: */ + MODULEEND(); +} + +void ElementConnectivityUsage(void) { + _printf_(true,"\n"); + _printf_(true," usage: elementconnectivity = %s(elements, nodeconnectivity);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/ElementConnectivity/ElementConnectivity.h (revision 12168) @@ -0,0 +1,60 @@ +/* + ElementConnectivity.h +*/ + +#ifndef _ELEMENTCONNECTIVITY_H +#define _ELEMENTCONNECTIVITY_H + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +/*Header files: */ +#include "../../c/include/globals.h" +#include "../../c/toolkits/toolkits.h" +#include "../../c/include/include.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" +#include "../../c/io/io.h" +#include "../../c/EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +/* serial input macros: */ +#define ELEMENTS (mxArray*)prhs[0] +#define NODECONNECTIVITY (mxArray*)prhs[1] +/* serial output macros: */ +#define ELEMENTCONNECTIVITY (mxArray**)&plhs[0] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +/* serial input macros: */ +#define ELEMENTS PyTuple_GetItem(args,0) +#define NODECONNECTIVITY PyTuple_GetItem(args,1) +/* serial output macros: */ +#define ELEMENTCONNECTIVITY output,0 +#endif + +#undef __FUNCT__ +#define __FUNCT__ "ElementConnectivity" + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 2 + +/* local prototypes: */ +void ElementConnectivityUsage(void); + +#endif /* _ELEMENTCONNECTIVITY_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.cpp (revision 12168) @@ -0,0 +1,32 @@ +/*\file EnumToString.c + *\brief:convert enum (int) to string + */ + +#include "./EnumToString.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + char *name = NULL; + int enum_in; + + /*checks on arguments on the matlab side: */ + if(nrhs!=NRHS){ + EnumToStringUsage(); _error_(" usage. See above"); + } + + /*Fetch inputs: */ + FetchData(&enum_in,ENUMIN); + + /*Run core function: */ + EnumToStringx(&name,enum_in); + + /* output: */ + WriteData(NAME,name); +} + +void EnumToStringUsage(void) +{ + _printf_(true,"\n"); + _printf_(true," usage: %sstring = EnumToString(enum);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/EnumToString/EnumToString.h (revision 12168) @@ -0,0 +1,32 @@ +/*!\file: EnumToString.h + * \brief header file for EnumToString module. + */ + +#ifndef _ENUMTOSTRING_H +#define _ENUMTOSTRING_H + +/* local prototypes: */ +void EnumToStringUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +/* serial input macros: */ +#define ENUMIN (mxArray*)prhs[0] + +/* serial output macros: */ +#define NAME (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 1 + +#undef __FUNCT__ +#define __FUNCT__ "EnumToString" + +#endif /* _TEST_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.cpp (revision 12168) @@ -0,0 +1,98 @@ +/*\file Exp2Kml.c + *\brief: exp to kml file conversion mex module. + */ +#include "./Exp2Kml.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,verbose=1; + + /*input: */ + char *filexp=NULL,*filkml=NULL; + int sgn; + + Options* options=NULL; + char *choles=NULL; + bool holes=false; + double cm=0.,sp=0.; + + /* output: */ + int iret=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + Exp2KmlUsage(); _error_("Exp2Kml usage error"); + } + if (nrhs < NRHS) { + Exp2KmlUsage(); _error_("Exp2Kml usage error"); + } + + /*Input datasets: */ + FetchData(&filexp,EXP_IN); + FetchData(&filkml,KML_IN); + FetchData(&sgn,SGN_IN); + FetchData(&options,NRHS,nrhs,prhs); + + options->Get(&choles,"holes","no"); + if (!strncmp(choles,"y",1) || !strncmp(choles,"on",2)) holes=true; + + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); + if (verbose) printf(" sp=%g\n",sp); + } + + /*some checks*/ + if (sgn !=+1 && sgn !=-1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) + iret=Exp2Kmlx(filexp,filkml,sgn,cm,sp,holes); + else + iret=Exp2Kmlx(filexp,filkml,sgn,holes); + + /*Write data: */ + WriteData(RET_OUT,iret); + + /*Clean-up*/ + xfree((void**)&choles); + delete options; + xfree((void**)&filkml); + xfree((void**)&filexp); + + /*end module: */ + MODULEEND(); +} + +void Exp2KmlUsage(void){ + _printf_(true,"Exp2Kml - exp to kml file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from exp to kml format.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [ret]=Exp2Kml(filexp,filkml,sgn,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," filexp file name of exp file to be read (char)\n"); + _printf_(true," filkml file name of kml file to be written (char)\n"); + _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); + _printf_(true,"\n"); + _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); + _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); + _printf_(true," holes flag for treatment of multiple profiles (char, optional, 'yes' for holes))\n"); + _printf_(true,"\n"); + _printf_(true," ret return code (non-zero for warning)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [ret]=Exp2Kml('file.exp','file.kml', 1);\n"); + _printf_(true," [ret]=Exp2Kml('file.exp','file.kml', 1,'central_meridian',45,'standard_parallel',70,'holes','yes');\n"); + _printf_(true," [ret]=Exp2Kml('file.exp','file.kml',-1,'central_meridian', 0,'standard_parallel',71,'holes','yes');\n"); + _printf_(true,"\n"); +} + Index: /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Exp2Kml/Exp2Kml.h (revision 12168) @@ -0,0 +1,36 @@ +/*!\file Exp2Kml.h + * \brief: prototype for exp to kml file conversion mex module. + */ + +#ifndef _EXP2KML_H +#define _EXP2KML_H + +/* local prototypes: */ +void Exp2KmlUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Exp2Kml" + + +/* serial input macros: */ +#define EXP_IN prhs[0] +#define KML_IN prhs[1] +#define SGN_IN prhs[2] + +/* serial output macros: */ +#define RET_OUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 3 +#undef NLHS +#define NLHS 1 + +#endif + Index: /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.cpp (revision 12168) @@ -0,0 +1,69 @@ +/*!\file: HoleFiller.cpp + * \brief fill holes in matlab velocity array + this matlab module is an adaptation of a routine written by Robber + Crippen. The original routine was designed for the SRTM mission at JPL, + and can be found in the current directory, under the name + HoleFillerCrippen. It fills void holes in an image, using an interpolation + algorithm, and optionnally a smoothing algorithm. + This matlab module extends the Crippen routine to be used in Matlab, + using double arrays found in the workspace, and loaded directly into memory. +*/ + + +#include "./HoleFiller.h" + +void mexFunction( int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + int i,j; + + /* required input: */ + double* imagein=NULL; + int imagein_rows,imagein_cols; + int smooth_flag; + int smooth; + + + /* output: */ + mxArray* pfield=NULL; + double* imageout=NULL; + int imageout_rows,imageout_cols; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&HoleFillerUsage); + + /*Fetch data: */ + FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN); + FetchData(&smooth_flag,SMOOTH); + + /*Get smooth flag setup: */ + if (smooth_flag==0) + smooth=1; + else + smooth=0; + + /*Run core hole filler routine: */ + HoleFillerx( &imageout,imagein,imagein_rows,imagein_cols,smooth); + + /* output: */ + WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols); + + /*end module: */ + MODULEEND(); +} + + +void HoleFillerUsage(void) +{ + printf(" HoleFiller usage:\n"); + printf(" [image_out]=HoleFiller(image_in,smooth);\n\n"); + printf(" where:\n"); + printf(" image_in in double format\n"); + printf(" smooth: 1 to smooth with a box filer, 0 to leave data raw\n"); + printf(" image_out in double format\n"); + printf("\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/HoleFiller/HoleFiller.h (revision 12168) @@ -0,0 +1,36 @@ + +/* + HoleFiller.h +*/ + + +#ifndef _HOLEFILLER_H +#define _HOLEFILLER_H + +/* local prototypes: */ +void HoleFillerUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "HoleFiller" + + +/* serial input macros: */ +#define IMAGEIN prhs[0] +#define SMOOTH prhs[1] + +/* serial output macros: */ +#define IMAGEOUT &plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 2 + +#endif /* _HOLEFILLER_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/InternalFront/InternalFront.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InternalFront/InternalFront.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InternalFront/InternalFront.cpp (revision 12168) @@ -0,0 +1,99 @@ +/*\file InternalFront.c + *\brief: build pressureload + */ + +#include "./InternalFront.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + bool* elementonwater=NULL; + int* elements=NULL; + int* connectivity=NULL; + int* elementconnectivity=NULL; + int* front=NULL; + double* front2=NULL; + bool found; + int numberofelements,numberofsegments; + int N,M; + int i,j,ii,jj,id; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InternalFrontUsage); + + /*Fetch required fields*/ + FetchData(&numberofelements,mxGetAssignedField(MODEL,0,"numberofelements")); + if(numberofelements<=0) _error_("No elements found in the model"); + FetchData(&elements,&M,&N,mxGetAssignedField(MODEL,0,"elements")); + if(M!=numberofelements || N!=3) _error_("Field 'elements' should be of size [md.numberofelements 3]"); + FetchData(&elementonwater,&M,&N,mxGetAssignedField(MODEL,0,"elementonwater")); + if(M!=numberofelements || N!=1) _error_("Field 'elementonwater' should be of size [md.numberofelements 1]"); + FetchData(&elementconnectivity,&M,&N,mxGetAssignedField(MODEL,0,"elementconnectivity")); + if(M!=numberofelements || N!=3) _error_("Field 'elementconnectivity' should be of size [md.numberofelements 3]"); + + /*Allocate and initialize all variables*/ + numberofsegments=0; + front=(int*)xmalloc(3*numberofelements*4*sizeof(int)); + + /*Loop over all elements on water*/ + for(i=0;i=7){ + /*default values: */ + FetchData(&default_values,&num_default_values,DEFAULTHANDLE); + } + else{ + default_values=NULL; + num_default_values=0; + } + + if(nrhs>=8){ + + /*Call expread on filename to build a contour array in the matlab workspace: */ + mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); + + /*contours: */ + numcontours=mxGetNumberOfElements(matlabstructure); + contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. + contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); + contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); + *(contours+i)=contouri; + } + + /* Debugging of contours :{{{1*/ + /*for(i=0;inods); + for (j=0;jnods;j++){ + printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); + } + }*/ + /*}}}*/ + } + else{ + numcontours=0; + contours=NULL; + } + + + /*some checks*/ + if (x_data_rows!=y_data_rows){ + _error_("vectors x and y should have the same length!"); + } + if (x_prime_rows!=y_prime_rows){ + _error_("vectors x_prime and y_prime should have the same length!"); + } + + /*get number of elements and number of nodes in the data*/ + nels_data=index_data_rows; + nods_data=x_data_rows; + nods_prime=x_prime_rows; + + /* Run core computations: */ + InterpFromMesh2dx(&data_prime,index_data,x_data,y_data,nods_data,nels_data,data,data_rows,x_prime,y_prime,nods_prime,default_values,num_default_values,contours,numcontours); + + /*Write data: */ + WriteData(DATAPRIME,data_prime); + + /*end module: */ + MODULEEND(); +} + +void InterpFromMesh2dUsage(void) +{ + _printf_(true," usage:\n"); + _printf_(true," data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime);\n\n"); + _printf_(true," or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value);\n\n"); + _printf_(true," or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value,contourname);\n\n"); + _printf_(true," where:\n"); + _printf_(true," x,y: coordinates of the nodes where data is defined\n"); + _printf_(true," index: index of the mesh where data is defined\n"); + _printf_(true," data - vector holding the data to be interpolated onto the points.\n"); + _printf_(true," x_prime,y_prime: coordinates of the mesh vertices onto which we interpolate.\n"); + _printf_(true," default_value: a scalar or vector of size length(x_prime).\n"); + _printf_(true," contourname: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.\n"); + _printf_(true," data_prime: vector of prime interpolated data.\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMesh2d/InterpFromMesh2d.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMesh2d/InterpFromMesh2d.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMesh2d/InterpFromMesh2d.h (revision 12168) @@ -0,0 +1,40 @@ +/*!\file InterpFromMesh2d.h + * \brief: prototype for Data Interpolation mex module. + */ + +#ifndef _INTERPFROMMESH2D_H +#define _INTERPFROMMESH2D_H + +/* local prototypes: */ +void InterpFromMesh2dUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "InterpFromMesh2d" + +#undef CLEANUP +#define CLEANUP InterpFromMesh2dLocalCleanup(); + +/* serial input macros: */ +#define INDEXHANDLE prhs[0] +#define XHANDLE prhs[1] +#define YHANDLE prhs[2] +#define DATAHANDLE prhs[3] +#define XPRIMEHANDLE prhs[4] +#define YPRIMEHANDLE prhs[5] +#define DEFAULTHANDLE prhs[6] +#define FILENAME prhs[7] + +/* serial output macros: */ +#define DATAPRIME (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 + +#endif /* _INTERPFROMMESH2D_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp (revision 12168) @@ -0,0 +1,79 @@ +/*\file InterpFromMeshToGrid.c + *\brief: compute diff between observed and modeled velocity + */ + +#include "./InterpFromMeshToGrid.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ + double* index=NULL; + int nel; + double* x=NULL; + int nods; + double* y=NULL; + double* meshdata=NULL; + int meshdata_length; + double xmin; + double ymax; + double xposting; + double yposting; + int nlines,ncols; + double default_value; + + /* output datasets: */ + double* griddata=NULL; + double* x_m=NULL; + double* y_m=NULL; + + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InterpFromMeshToGridUsage); + + /*Input datasets: */ + FetchData(&index,&nel,NULL,INDEX); + FetchData(&x,&nods,NULL,X); + FetchData(&y,NULL,NULL,Y); + FetchData(&meshdata,&meshdata_length,NULL,MESHDATA); + FetchData(&xmin,XMIN); + FetchData(&ymax,YMAX); + FetchData(&xposting,XPOSTING); + FetchData(&yposting,YPOSTING); + FetchData(&nlines,NLINES); + FetchData(&ncols,NCOLS); + FetchData(&default_value,DEFAULTVALUE); + + /*Call core of computation: */ + InterpFromMeshToGridx(&x_m,&y_m,&griddata,index,x,y,nods,nel,meshdata,meshdata_length,xmin,ymax,xposting,yposting,nlines,ncols,default_value); + + /*Write results: */ + WriteData(XM,x_m,ncols); + WriteData(YM,y_m,nlines); + WriteData(GRIDDATA,griddata,nlines,ncols); + + /*Free ressources: */ + //let matlab do this. + + /*end module: */ + MODULEEND(); +} + +void InterpFromMeshToGridUsage(void) +{ + _printf_(true,"INTERPFROMMESHTOGRID - interpolation of a data defined on a mesh onto a grid\n"); + _printf_(true,"\n"); + _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); + _printf_(true," defined on a triangular mesh onto a regular grid\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [x_m,y_m,griddata]=InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value)\n"); + _printf_(true,"\n"); + _printf_(true," index,x,y: delaunay triangulation defining the mesh.\n"); + _printf_(true," meshdata: vertex values of data to be interpolated.\n"); + _printf_(true," xmin,ymax,posting,nlines,ncols: parameters that define the grid\n"); + _printf_(true," default_value: value of points located out of the mesh.\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 12168) @@ -0,0 +1,46 @@ + +/* + InterpFromMeshToGrid.h +*/ + + +#ifndef _INTERPFROMMESHTOGRID_H +#define _INTERPFROMMESHTOGRID_H + +/* local prototypes: */ +void InterpFromMeshToGridUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "InterpFromMeshToGrid" + +/* serial input macros: */ +#define INDEX (mxArray*)prhs[0] +#define X (mxArray*)prhs[1] +#define Y (mxArray*)prhs[2] +#define MESHDATA (mxArray*)prhs[3] +#define XMIN (mxArray*)prhs[4] +#define YMAX (mxArray*)prhs[5] +#define XPOSTING (mxArray*)prhs[6] +#define YPOSTING (mxArray*)prhs[7] +#define NLINES (mxArray*)prhs[8] +#define NCOLS (mxArray*)prhs[9] +#define DEFAULTVALUE (mxArray*)prhs[10] + +/* serial output macros: */ +#define XM (mxArray**)&plhs[0] +#define YM (mxArray**)&plhs[1] +#define GRIDDATA (mxArray**)&plhs[2] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 3 +#undef NRHS +#define NRHS 11 + +#endif /* _INTERPFROMMESHTOGRID_H*/ Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12168) @@ -0,0 +1,119 @@ +/*\file InterpFromMeshToMesh2d.c + *\brief: bamg module. + */ +#include "./InterpFromMeshToMesh2d.h" + + +WRAPPER(InterpFromMeshToMesh2d){ + + /*input: */ + double* index=NULL; + int index_cols; + double* x_data=NULL; + int x_data_rows; + double* y_data=NULL; + int y_data_rows; + double* data=NULL; + int data_rows; + int data_cols; + double* x_interp=NULL; + int x_interp_rows; + double* y_interp=NULL; + int y_interp_rows; + char* contourname=NULL; + double* default_values=NULL; + int num_default_values=0; + DataSet *contours = NULL; + + /*Intermediary*/ + int nels_data; + + /* output: */ + double* data_interp=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on output arguments on the matlab side: */ + #ifdef _HAVE_MATLAB_MODULES_ + if(nlhs!=NLHS){ + InterpFromMeshToMesh2dUsage(); + _error_("InterpFromMeshToMesh2dUsage usage error"); + } + #endif + /*check on input arguments: */ + if((nrhs!=6) & (nrhs!=8)){ + InterpFromMeshToMesh2dUsage(); + _error_("InterpFromMeshToMesh2dUsage usage error"); + } + + /*Input datasets: */ + FetchData(&index,&nels_data,&index_cols,INDEX); + FetchData(&x_data,&x_data_rows,NULL,X); + FetchData(&y_data,&y_data_rows,NULL,Y); + FetchData(&data,&data_rows,&data_cols,DATA); + FetchData(&x_interp,&x_interp_rows,XINTERP); + FetchData(&y_interp,&y_interp_rows,YINTERP); + + /*Figure out contours and default values: */ + if(nrhs==8){ + FetchData(&default_values,&num_default_values,DEFAULT); + FetchData(&contourname,CONTOURNAME); + contours=DomainOutlineRead(contourname); + } + else{ + num_default_values=0; + default_values=NULL; + contours=new DataSet(); + } + + + /*some checks*/ + if (x_data_rows!=y_data_rows){ + _error_("vectors x and y should have the same length!"); + } + if (x_interp_rows!=y_interp_rows){ + _error_("vectors x_interp and y_interp should have the same length!"); + } + if (index_cols!=3){ + _error_("index should have 3 columns (input provided has %i columns)",index_cols); + } + + /* Run core computations: */ + InterpFromMeshToMesh2dx(&data_interp,index,x_data,y_data,x_data_rows,nels_data,data,data_rows,data_cols,x_interp,y_interp,x_interp_rows,default_values,num_default_values,contours); + + /*Write data: */ + WriteData(DATAINTERP,data_interp,x_interp_rows,data_cols); + + /*end module: */ + MODULEEND(); +} + +void InterpFromMeshToMesh2dUsage(void)//{{{1 + +{ + _printf_(true,"INTERFROMMESHTOMESH2D - interpolation from a 2d triangular mesh onto a list of point\n"); + _printf_(true,"\n"); + _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); + _printf_(true," defined on a triangular mesh onto a list of point\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp);\n"); + _printf_(true," or data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp,default_value,contourname);\n"); + _printf_(true,"\n"); + _printf_(true," index: index of the mesh where data is defined\n"); + _printf_(true," x,y: coordinates of the nodes where data is defined\n"); + _printf_(true," data: matrix holding the data to be interpolated onto the mesh. (one column per field)\n"); + _printf_(true," x_interp,y_interp: coordinates of the points onto which we interpolate.\n"); + _printf_(true," if default_value and contourname not specified: linear interpolation will happen on all x_interp,y_interp.\n"); + _printf_(true," if (default_value,contourname) specified: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.\n"); + _printf_(true," note that default_value is either a scalar, or a vector of size length(x_interp)\n"); + _printf_(true," data_interp: vector of mesh interpolated data.\n"); + _printf_(true,"\n"); + _printf_(true," Example:\n"); + _printf_(true," load('temperature.mat');\n"); + _printf_(true," md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y);\n"); + _printf_(true," md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y,253,'Contour.exp');\n"); + _printf_(true,"\n"); +} +//}}} Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12168) @@ -0,0 +1,71 @@ +/*!\file InterpFromMeshToMesh2d.h + * \brief: prototype for Data Interpolation mex module. + */ + +#ifndef _INTERPFROMMESHTOMESH2d_H +#define _INTERPFROMMESHTOMESH2d_H + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +/*Header files: */ +#include "../../c/include/globals.h" +#include "../../c/toolkits/toolkits.h" +#include "../../c/include/include.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" +#include "../../c/io/io.h" +#include "../../c/EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define INDEX prhs[0] +#define X prhs[1] +#define Y prhs[2] +#define DATA prhs[3] +#define XINTERP prhs[4] +#define YINTERP prhs[5] +#define DEFAULT prhs[6] +#define CONTOURNAME prhs[7] + +/* serial output macros: */ +#define DATAINTERP (mxArray**)&plhs[0] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define INDEX PyTuple_GetItem(args,0) +#define X PyTuple_GetItem(args,1) +#define Y PyTuple_GetItem(args,2) +#define DATA PyTuple_GetItem(args,3) +#define XINTERP PyTuple_GetItem(args,4) +#define YINTERP PyTuple_GetItem(args,5) +#define DEFAULT PyTuple_GetItem(args,6) +#define CONTOURNAME PyTuple_GetItem(args,7) +/* serial output macros: */ +#define DATAINTERP output,0 +#endif + +#undef __FUNCT__ +#define __FUNCT__ "InterpFromMeshToMesh2d" + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 6 //can be 8 though + +/* local prototypes: */ +void InterpFromMeshToMesh2dUsage(void); + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 12168) @@ -0,0 +1,119 @@ +/*!\file InterpFromMeshToMesh3d.c + * \brief: data interpolation from a list of (x,y,values) into mesh vertices + + InterpFromMeshToMesh3d.c + + usage: + data_mesh=InterpFromMeshToMesh3d(index,x,y,z,data,x_mesh,y_mesh,z_mesh); + + where: + + input: + x,y,z: coordinates of matrix data + data - matrix holding the data to be interpolated onto the mesh. + x_mesh,y_mesh,z_mesh: coordinates of the mesh vertices onto which we interpolate. + + output: + data_mesh: vector of mesh interpolated data. + +*/ + +#include "./InterpFromMeshToMesh3d.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + + /*input: */ + double* index_data=NULL; + int index_data_rows; + + double* x_data=NULL; + double* y_data=NULL; + double* z_data=NULL; + + int x_data_rows; + int y_data_rows; + int z_data_rows; + + double* data=NULL; + int data_rows; + int data_cols; + + double* x_prime=NULL; + double* y_prime=NULL; + double* z_prime=NULL; + + int x_prime_rows; + int y_prime_rows; + int z_prime_rows; + + double default_value; + + /*Intermediary*/ + int nods_data; + int nels_data; + int nods_prime; + + /* output: */ + Vector* data_prime=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InterpFromMeshToMesh3dUsage); + + /*Input datasets: */ + FetchData(&index_data,&index_data_rows,NULL,INDEXHANDLE); + FetchData(&x_data,&x_data_rows,NULL,XHANDLE); + FetchData(&y_data,&y_data_rows,NULL,YHANDLE); + FetchData(&z_data,&z_data_rows,NULL,ZHANDLE); + FetchData(&data,&data_rows,&data_cols,DATAHANDLE); + FetchData(&x_prime,&x_prime_rows,NULL,XPRIMEHANDLE); + FetchData(&y_prime,&y_prime_rows,NULL,YPRIMEHANDLE); + FetchData(&z_prime,&z_prime_rows,NULL,ZPRIMEHANDLE); + FetchData(&default_value,DEFAULTHANDLE); + + /*some checks*/ + if (x_data_rows!=y_data_rows || x_data_rows!=z_data_rows){ + _error_("vectors x, y and z should have the same length!"); + } + if (x_prime_rows!=y_prime_rows || x_prime_rows!=z_prime_rows){ + _error_("vectors x_prime, y_prime and z_prime should have the same length!"); + } + /*get number of elements and number of nodes in the data*/ + nels_data=index_data_rows; + nods_data=x_data_rows; + nods_prime=x_prime_rows; + + /* Run core computations: */ + InterpFromMeshToMesh3dx(&data_prime,index_data,x_data,y_data,z_data,nods_data,nels_data,data,data_rows,x_prime,y_prime,z_prime,nods_prime,default_value); + + /*Write data: */ + WriteData(DATAPRIME,data_prime); + + /*end module: */ + MODULEEND(); +} + +void InterpFromMeshToMesh3dUsage(void) +{ + _printf_(true,"INTERPFROMMESHTOMESH3D - interpolation from a 3d hexahedron mesh onto a list of point\n"); + _printf_(true,"\n"); + _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); + _printf_(true," defined on a triangular mesh onto a list of point\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," data_prime=InterpFromMeshToMesh3d(index,x,y,z,data,x_prime,y_prime,z_prime,default_value);\n"); + _printf_(true,"\n"); + _printf_(true," index: index of the mesh where data is defined\n"); + _printf_(true," x,y,z: coordinates of the nodes where data is defined\n"); + _printf_(true," data: matrix holding the data to be interpolated onto the mesh.\n"); + _printf_(true," x_prime,y_prime,z_prime: coordinates of the points onto which we interpolate.\n"); + _printf_(true," default_value: default value if no data is found (holes).\n"); + _printf_(true," data_prime: vector of mesh interpolated data.\n"); + _printf_(true,"\n"); + _printf_(true," Example:\n"); + _printf_(true," load('temperature.mat');\n"); + _printf_(true," md.initialization.temperature=InterpFromMeshToMesh3d(index,x,y,z,temperature,md.mesh.x,md.mesh.y,md.mesh.z,253);\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 12168) @@ -0,0 +1,44 @@ +/*!\file InterpFromMeshToMesh3d.h + * \brief: prototype for Data Interpolation mex module. + */ + +#ifndef _INTERPFROMMESH3D_H +#define _INTERPFROMMESH3D_H + +/* local prototypes: */ +void InterpFromMeshToMesh3dUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "InterpFromMeshToMesh3d" + +#undef CLEANUP +#define CLEANUP InterpFromMeshToMesh3dLocalCleanup(); + + +/* serial input macros: */ +#define INDEXHANDLE prhs[0] +#define XHANDLE prhs[1] +#define YHANDLE prhs[2] +#define ZHANDLE prhs[3] +#define DATAHANDLE prhs[4] +#define XPRIMEHANDLE prhs[5] +#define YPRIMEHANDLE prhs[6] +#define ZPRIMEHANDLE prhs[7] +#define DEFAULTHANDLE prhs[8] + +/* serial output macros: */ +#define DATAPRIME (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 9 + +#endif /* _INTERPFROMMESHTOMESH3D_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.cpp (revision 12168) @@ -0,0 +1,129 @@ +/*\file KMLFileRead.c + *\brief: KML file reader module. + */ +#include "./KMLFileRead.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,j,nnodes=0,verbose=1; + KML_Object* kobj; + + /*input: */ + char* name=NULL; + char* notes=NULL; + const mxArray* notesi; + mwIndex nindex; + int* elem=NULL; + int melem=0,nelem=0; + int* nodecon=NULL; + int mncon=0,nncon=0; + double* lat=NULL; + int mlat=0,nlat=0,llat=0; + double* lng=NULL; + int mlng=0,nlng=0,llng=0; + int nparts=0; + int* part=NULL; + int mprt=0,nprt=0,lprt=0; + double* data=NULL; + int mdata=0,ndata=0; + double* cmap=NULL; + int mcmap=0,ncmap=0; + char* filnam=NULL; + FILE* fidi=NULL; + FILE* fido=NULL; + Options* options=NULL; + char* echo =NULL; + char* deepecho=NULL; + char* write =NULL; + + /* output: */ + int ierror=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + KMLFileReadUsage(); _error_("KMLFileRead usage error"); + } + if (nrhs < NRHS) { + KMLFileReadUsage(); _error_("KMLFileRead usage error"); + } + + /*Input datasets: */ + FetchData(&filnam,FILENAME); + FetchData(&options,NRHS,nrhs,prhs); + FetchData(&options,NRHS,nrhs,prhs); + + options->Get(&echo ,"echo" ,"off"); + options->Get(&deepecho,"deepecho","off"); + options->Get(&write ,"write" ,"off"); + + /*some checks*/ + if (!strlen(filnam)) strcpy(filnam,"stdout"); + + if (verbose) printf("Opening file \"%s\".\n",filnam); + fidi=fopen(filnam,"r"); + + /* Run core computations: */ + if (verbose) printf("Calling core:\n"); + kobj=KMLFileReadx(fidi); + + if (verbose) printf("Closing file \"%s\".\n",filnam); + fclose(fidi); + + if (kobj){ + if (!strncmp(echo ,"on",2) || !strncmp(echo ,"y",1)) + kobj->Echo(); + if (!strncmp(deepecho,"on",2) || !strncmp(deepecho,"y",1)) + kobj->DeepEcho(); + if (strncmp(write,"off",3) && strncmp(write,"no",2)) { + if (!strncmp(write,"on",2) || !strncmp(write,"yes",3) || !strncmp(write,"stdout",6)) { + kobj->Write(stdout,""); + } + else { + if (verbose) printf("Opening file \"%s\".\n",write); + fido=fopen(write,"w"); + kobj->Write(fido,""); + if (verbose) printf("Closing file \"%s\".\n",write); + ierror=fclose(fido); + } + } + delete kobj; + } + + /*Write data: */ + WriteData(ERRORFLAG,ierror); + + /*Clean-up*/ + xfree((void**)&write); + xfree((void**)&deepecho); + xfree((void**)&echo); + delete options; + + /*end module: */ + MODULEEND(); +} + +void KMLFileReadUsage(void){ + _printf_(true,"KMLFileRead - KML file reader module:\n"); + _printf_(true,"\n"); + _printf_(true," This module reads a KML file.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [ierror]=KMLFileRead(kmlfile,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," kmlfile file name of kml file to be read (char)\n"); + _printf_(true,"\n"); + _printf_(true," echo echo command (char, optional, 'off'/'on')\n"); + _printf_(true," deepecho deep echo command (char, optional, 'off'/'on')\n"); + _printf_(true," write write command (char, optional, 'off'/'stdout'/kmlfile)\n"); + _printf_(true,"\n"); + _printf_(true," ierror return code (non-zero for error)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [ierror]=KMLFileRead('file.kml','deepecho','on');\n"); + _printf_(true," [ierror]=KMLFileRead('filin.kml','echo','on','write','filout.kml');\n"); + _printf_(true,"\n"); +} + Index: /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLFileRead/KMLFileRead.h (revision 12168) @@ -0,0 +1,33 @@ +/*!\file KMLFileRead.h + * \brief: prototype for KML file reader mex module. + */ + +#ifndef _KMLFILEREAD_H +#define _KMLFILEREAD_H + +/* local prototypes: */ +void KMLFileReadUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "KMLFileRead" + + +/* serial input macros: */ +#define FILENAME prhs[0] + +/* serial output macros: */ +#define ERRORFLAG (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 1 +#undef NLHS +#define NLHS 1 + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12168) @@ -0,0 +1,143 @@ +/*\file KMLMeshWrite.c + *\brief: KML mesh writer module. + */ +#include "./KMLMeshWrite.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,j,nnodes=0,verbose=1; + + /*input: */ + char* name=NULL; + char* notes=NULL; + const mxArray* notesi; + mwIndex nindex; + int* elem=NULL; + int melem=0,nelem=0; + int* nodecon=NULL; + int mncon=0,nncon=0; + double* lat=NULL; + int mlat=0,nlat=0,llat=0; + double* lng=NULL; + int mlng=0,nlng=0,llng=0; + int nparts=0; + int* part=NULL; + int mprt=0,nprt=0,lprt=0; + double* data=NULL; + int mdata=0,ndata=0; + double* cmap=NULL; + int mcmap=0,ncmap=0; + char* filnam=NULL; + FILE* fid=NULL; + Options* options=NULL; + + /* output: */ + int ierror=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + KMLMeshWriteUsage(); _error_("KMLMeshWrite usage error"); + } + if (nrhs < NRHS) { + KMLMeshWriteUsage(); _error_("KMLMeshWrite usage error"); + } + + /*Input datasets: */ + FetchData(&name,NAME); + +/* notes is typically a cell array of character strings */ + if (mxIsCell(NOTES)) { + for (nindex=0; nindexnnodes) nnodes=elem[i]; + if(part) for (i=0; i nparts) nparts=part[i]+1; + + if (nodecon && (mncon != nnodes)) + _error_("Nodal connectivity table, if supplied, must be supplied for all nodes."); + else if (!nodecon) + mncon=nnodes; + if ((llat != nnodes) || (llng != nnodes) || (llat != llng)) + _error_("Latitude and longitude vectors must be supplied for all nodes."); + if (part && (lprt != nnodes)) + _error_("Partitioning vector, if supplied, must be supplied for all nodes."); + if (data && !((mdata == nnodes) || (mdata == melem))) + _error_("Data matrix, if supplied, must be supplied for all nodes or all elements."); + if (cmap && (ncmap != 3)) + _error_("Colormap matrix, if supplied, must have three columns for rgb."); + if (!strlen(filnam)) + strcpy(filnam,"stdout"); + + /* Run core computations: */ + fid=fopen(filnam,"w"); + KMLMeshWritex(&ierror,name,notes,elem,melem,nelem,nodecon,mncon,nncon,lat,lng,part,data,mdata,ndata,cmap,mcmap,ncmap,fid); + fclose(fid); + + /*Write data: */ + WriteData(ERRORFLAG,ierror); + + /*Clean-up*/ + delete options; + if (mxIsCell(NOTES) && notes) xfree((void**)¬es); + + /*end module: */ + MODULEEND(); +} + +void KMLMeshWriteUsage(void){ + _printf_(true,"KMLMeshWrite - KML mesh writer module:\n"); + _printf_(true,"\n"); + _printf_(true," This module writes the mesh of a model as KML polygons into the specified KML file.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," ierror=KMLMeshWrite(name,notes,elem,nodecon,lat,long,part,data,cmap,kmlfile);\n"); + _printf_(true,"\n"); + _printf_(true," name model name (string, may be empty)\n"); + _printf_(true," notes model notes (string or cell array of strings, may be empty)\n"); + _printf_(true," elem elements (double array)\n"); + _printf_(true," nodecon nodal connectivity array (double array, may be empty)\n"); + _printf_(true," lat nodal latititudes (double vector)\n"); + _printf_(true," long nodal longitudes (double vector)\n"); + _printf_(true," part nodal partitions (double vector, may be empty)\n"); + _printf_(true," data nodal or element data (double vector, may be empty)\n"); + _printf_(true," cmap color map (double nx3 array, may be empty)\n"); + _printf_(true," kmlfile KML file name (string)\n"); + _printf_(true,"\n"); + _printf_(true," ierror error flag (double, non-zero for error)\n"); + _printf_(true,"\n"); + _printf_(true," Example:\n"); + _printf_(true," KMLMeshWrite(md.name,md.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.part,md.fm_criterion,options.cmap,filekml);\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLMeshWrite/KMLMeshWrite.h (revision 12168) @@ -0,0 +1,42 @@ +/*!\file KMLMeshWrite.h + * \brief: prototype for KML mesh writer mex module. + */ + +#ifndef _KMLMESHWRITE_H +#define _KMLMESHWRITE_H + +/* local prototypes: */ +void KMLMeshWriteUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "KMLMeshWrite" + + +/* serial input macros: */ +#define NAME prhs[0] +#define NOTES prhs[1] +#define ELEMHANDLE prhs[2] +#define NODECONHANDLE prhs[3] +#define LATHANDLE prhs[4] +#define LNGHANDLE prhs[5] +#define PARTHANDLE prhs[6] +#define DATAHANDLE prhs[7] +#define CMAPHANDLE prhs[8] +#define FILENAME prhs[9] + +/* serial output macros: */ +#define ERRORFLAG (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 10 +#undef NLHS +#define NLHS 1 + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.cpp (revision 12168) @@ -0,0 +1,134 @@ +/*\file KMLOverlay.c + *\brief: KML file overlay mex module. + */ +#include "./KMLOverlay.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,verbose=1; + + /*input: */ + char* filkml=NULL; + char* filkmz=NULL; + + FILE* fid=NULL; + + Options* options=NULL; + int nlat=0,nlong=0; + double* lataxis =NULL; + double* longaxis=NULL; + int nimages=0; + char** pimages=NULL; + double dzip=0; + char* czip=NULL; + + /* output: */ + int ierror=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if(nlhs>NLHS){ + KMLOverlayUsage(); _error_("KMLOverlay usage error"); + } + if(nrhsGet(&lataxis ,&nlat ,"lataxis" ); + if (verbose && lataxis) for (i=0; iGet(&longaxis,&nlong,"longaxis"); + if (verbose && longaxis) for (i=0; iGet(&pimages,&nimages,"images"); + if (verbose && pimages) for (i=0; iGet(&dzip,"zip",0.); + if (verbose) printf(" dzip=%g\n",dzip); + + /*some checks*/ + if (nlat !=2) _error_("Latitudinal axes \"lataxis\" require two double values, not %d.",nlat); + if (nlong!=2) _error_("Longitudinal axes \"longaxis\" require two double values, not %d.",nlong); + if (!nimages) _error_("No image files provided."); + + if ((int)dzip){ + filkmz=filkml; + filkml=(char*)mxMalloc(8*sizeof(char)); + strcpy(filkml,"doc.kml"); + } + + if(!strlen(filkml)) strcpy(filkml,"stdout"); + + if(verbose) printf("Opening kml overlay file \"%s\".\n",filkml); + fid=fopen(filkml,"w"); + + /* Run core computations: */ + if (verbose) printf("Calling core:\n"); + KMLOverlayx(&ierror,lataxis,longaxis,nimages,pimages,fid); + + if (verbose) printf("Closing file \"%s\".\n",filkml); + fclose(fid); + + /* Create kmz file, if specified: */ + if ((int)dzip) { + czip=(char*)mxMalloc((5+strlen(filkmz)+1+strlen(filkml)+1)*sizeof(char)); + czip[0]='\0'; + strcat(czip,"!zip "); + strcat(czip,filkmz); + strcat(czip," "); + strcat(czip,filkml); + for (i=0; i0; i--) xfree((void**)&(pimages[i-1])); + xfree((void**)&pimages); + } + xfree((void**)&longaxis); + xfree((void**)&lataxis); + delete options; + xfree((void**)&filkml); + + /*end module: */ + MODULEEND(); +} + +void KMLOverlayUsage(void){ + _printf_(true,"KMLOverlay - KML file overlay module:\n"); + _printf_(true,"\n"); + _printf_(true," This module reads a list of image files and writes a KML or KMZ overlay file.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," ierror=KMLOverlay(kmlfile,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," kmlfile KML or KMZ file name (string)\n"); + _printf_(true,"\n"); + _printf_(true," lataxis latitude axis (double vector [south north], required)\n"); + _printf_(true," longaxis longitude axis (double vector [west east], required)\n"); + _printf_(true," images relative or http image file names (string or array of strings or cell array of strings, required)\n"); + _printf_(true," zip flag to zip the doc.kml and image files into kmzfile (double, non-zero for kmz)\n"); + _printf_(true,"\n"); + _printf_(true," ierror error flag (double, non-zero for error)\n"); + _printf_(true,"\n"); + _printf_(true," Example:\n"); + _printf_(true," KMLOverlay(kmlfile,'lataxis',[south north],'longaxis',[west east],'images',{'file1.png','http://issm/file2.png'},'zip',1);\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/KMLOverlay/KMLOverlay.h (revision 12168) @@ -0,0 +1,33 @@ +/*!\file KMLOverlay.h + * \brief: prototype for KML file overlay mex module. + */ + +#ifndef _KMLOVERLAY_H +#define _KMLOVERLAY_H + +/* local prototypes: */ +void KMLOverlayUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "KMLOverlay" + + +/* serial input macros: */ +#define FILENAME prhs[0] + +/* serial output macros: */ +#define ERRORFLAG (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 1 +#undef NLHS +#define NLHS 1 + +#endif Index: /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.cpp (revision 12168) @@ -0,0 +1,90 @@ +/*\file Kml2Exp.c + *\brief: kml to exp file conversion mex module. + */ +#include "./Kml2Exp.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,verbose=1; + + /*input: */ + char *filkml=NULL,*filexp=NULL; + int sgn; + Options* options=NULL; + double cm=0.,sp=0.; + + /* output: */ + int iret=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + Kml2ExpUsage(); _error_("Kml2Exp usage error"); + } + if (nrhs < NRHS) { + Kml2ExpUsage(); _error_("Kml2Exp usage error"); + } + + /*Input datasets: */ + FetchData(&filkml,KML_IN); + FetchData(&filexp,EXP_IN); + FetchData(&sgn,SGN_IN); + FetchData(&options,NRHS,nrhs,prhs); + + /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); + if (verbose) printf(" sp=%g\n",sp); + } + + /*some checks*/ + if (sgn !=+1 && sgn!= -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) + iret=Kml2Expx(filkml,filexp,sgn,cm,sp); + else + iret=Kml2Expx(filkml,filexp,sgn); + + /*Write data: */ + WriteData(RET_OUT,iret); + + /*Clean-up*/ + delete options; + xfree((void**)&filexp); + xfree((void**)&filkml); + + /*end module: */ + MODULEEND(); +} + +void Kml2ExpUsage(void){ + _printf_(true,"Kml2Exp - kml to exp file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from kml to exp format.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [ret]=Kml2Exp(filexp,filkml,sgn,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," filkml file name of kml file to be read (char)\n"); + _printf_(true," filexp file name of exp file to be written (char)\n"); + _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); + _printf_(true,"\n"); + _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); + _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); + _printf_(true,"\n"); + _printf_(true," ret return code (non-zero for warning)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [ret]=Kml2Exp('file.kml','file.exp', 1);\n"); + _printf_(true," [ret]=Kml2Exp('file.kml','file.exp', 1,'central_meridian',45,'standard_parallel',70);\n"); + _printf_(true," [ret]=Kml2Exp('file.kml','file.exp',-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); +} + Index: /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Kml2Exp/Kml2Exp.h (revision 12168) @@ -0,0 +1,36 @@ +/*!\file Kml2Exp.h + * \brief: prototype for kml to exp file conversion mex module. + */ + +#ifndef _KML2EXP_H +#define _KML2EXP_H + +/* local prototypes: */ +void Kml2ExpUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Kml2Exp" + + +/* serial input macros: */ +#define KML_IN prhs[0] +#define EXP_IN prhs[1] +#define SGN_IN prhs[2] + +/* serial output macros: */ +#define RET_OUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 3 +#undef NLHS +#define NLHS 1 + +#endif + Index: /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp (revision 12168) @@ -0,0 +1,52 @@ +/*\file Kriging.c + *\brief: best linear predictor + */ +#include "./Kriging.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*Outputs*/ + double *x = NULL; + double *y = NULL; + double *observations = NULL; + double *x_interp = NULL; + double *y_interp = NULL; + double *predictions = NULL; + int n_interp,n,n_obs; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&KrigingUsage); + + /*Fetch inputs: */ + FetchData(&x,&n_obs,X); + FetchData(&y,&n,Y); if(n_obs!=n) _error_("x and y should have the same size"); + FetchData(&observations,&n,OBSERVATIONS); if(n_obs!=n) _error_("x and observations should have the same size"); + FetchData(&x_interp,&n_interp,XINTERP); + FetchData(&y_interp,&n,YINTERP); if(n_interp!=n) _error_("x_interp and y_interp should have the same size"); + + /*Call x layer*/ + Krigingx(&predictions,x,y,observations,n_obs,x_interp,y_interp,n_interp); + + /*Generate output Matlab Structures*/ + WriteData(PREDICTIONS,predictions,n_interp); + + /*Free ressources: */ + xfree((void**)&x); + xfree((void**)&y); + xfree((void**)&observations); + xfree((void**)&x_interp); + xfree((void**)&y_interp); + xfree((void**)&predictions); + + /*end module: */ + MODULEEND(); +} + +void KrigingUsage(void){ + _printf_(true,"\n"); + _printf_(true," usage: predictions=%s(x,y,observations,x_interp,y_interp);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h (revision 12168) @@ -0,0 +1,35 @@ +/* + KrigingUsage.h +*/ + +#ifndef _KRIGING_H_ +#define _KRIGING_H_ + +/* local prototypes: */ +void KrigingUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Kriging" + +/* serial input macros: */ +#define X (mxArray *)prhs[0] +#define Y (mxArray *)prhs[1] +#define OBSERVATIONS (mxArray *)prhs[2] +#define XINTERP (mxArray *)prhs[3] +#define YINTERP (mxArray *)prhs[4] + +/* serial output macros: */ +#define PREDICTIONS (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 5 + +#endif /* _KRIGING_H_ */ Index: /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.cpp (revision 12168) @@ -0,0 +1,98 @@ +/*\file Ll2xy.c + *\brief: lat/long to x/y coordinate mex module. + */ +#include "./Ll2xy.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,verbose=1; + + /*input: */ + double *lat=NULL,*lon=NULL; + int nlat,nlon,ncoord; + int sgn; + + Options* options=NULL; + double cm=0.,sp=0.; + + /* output: */ + double *x=NULL,*y=NULL; + int iret=0; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + Ll2xyUsage(); _error_("Ll2xy usage error"); + } + if (nrhs < NRHS) { + Ll2xyUsage(); _error_("Ll2xy usage error"); + } + + /*Input datasets: */ + FetchData(&lat,&nlat,LAT_IN); + FetchData(&lon,&nlon,LON_IN); + FetchData(&sgn,SGN_IN); + FetchData(&options,NRHS,nrhs,prhs); + + /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ + if(options->GetOption("central_meridian") || options->GetOption("standard_parallel")){ + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); + if (verbose) printf(" sp=%g\n",sp); + } + + /*some checks*/ + if (verbose) printf("Checking inputs:\n"); + if (nlat != nlon) _error_("Must have same number of lat[%d] and lon[%d] coordinates.",nlat,nlon); + else ncoord=nlat; + if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + x=(double*)mxMalloc(ncoord*sizeof(double)); + y=(double*)mxMalloc(ncoord*sizeof(double)); + + /* Run core computations: */ + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) + iret=Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + else + iret=Ll2xyx(x,y,lat,lon,ncoord,sgn); + + /*Write data: */ + WriteData(X_OUT,x,ncoord); + WriteData(Y_OUT,y,ncoord); + + /*Clean-up*/ + delete options; + + /*end module: */ + MODULEEND(); +} + +void Ll2xyUsage(void){ + _printf_(true,"Ll2xy - lat/long to x/y coordinate transformation module:\n"); + _printf_(true,"\n"); + _printf_(true," This module transforms lat/long to x/y coordinates.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [x,y]=Ll2xy(lat,lon,sgn,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," lat latitude coordinates (double vector)\n"); + _printf_(true," lon longitude coordinates (double vector)\n"); + _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); + _printf_(true,"\n"); + _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); + _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); + _printf_(true,"\n"); + _printf_(true," x x coordinates (double vector)\n"); + _printf_(true," y y coordinates (double vector)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [x,y]=Ll2xy(lat,lon, 1);\n"); + _printf_(true," [x,y]=Ll2xy(lat,lon, 1,'central_meridian',45,'standard_parallel',70);\n"); + _printf_(true," [x,y]=Ll2xy(lat,lon,-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Ll2xy/Ll2xy.h (revision 12168) @@ -0,0 +1,37 @@ +/*!\file Ll2xy.h + * \brief: prototype for lat/long to x/y coordinate mex module. + */ + +#ifndef _LL2XY_H +#define _LL2XY_H + +/* local prototypes: */ +void Ll2xyUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Ll2xy" + + +/* serial input macros: */ +#define LAT_IN prhs[0] +#define LON_IN prhs[1] +#define SGN_IN prhs[2] + +/* serial output macros: */ +#define X_OUT (mxArray**)&plhs[0] +#define Y_OUT (mxArray**)&plhs[1] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 3 +#undef NLHS +#define NLHS 2 + +#endif + Index: /issm/branches/trunk-jpl-damage/src/modules/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Makefile.am (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Makefile.am (revision 12168) @@ -0,0 +1,8 @@ +SUBDIRS = +if MATLAB +SUBDIRS += matlab +endif + +if PYTHON +SUBDIRS += python +endif Index: /issm/branches/trunk-jpl-damage/src/modules/MeshPartition/MeshPartition.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/MeshPartition/MeshPartition.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/MeshPartition/MeshPartition.cpp (revision 12168) @@ -0,0 +1,104 @@ +/*!\file: MeshPartition.cpp + * \brief: partition mesh according to number of areas, using Metis library. + + usage: + [element_partitioning,node_partitioning]=MeshPartition(model,numareas) + + %Info needed from model are the following: + %mesh info: + numberofelements,numberofvertices,elements,elements_width + %Non-extruded 2d mesh info + nel2d,nods2d,elements2d, + %Extruded 2d mesh info + nel2d_ext,nods2d_ext,elements2d_ext, + %Diverse + numberoflayers,dim) + + output: + vector of partitioning area numbers, for every element. + vector of partitioning area numbers, for every node. +*/ + +#include "./MeshPartition.h" + + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + + + /*Indexing: */ + int i,j; + + /* required input: */ + int dim; + int numberofelements; + int numberofvertices; + double *elements = NULL; + int elements_width; + + int numberofelements2d; + int numberofvertices2d; + double* elements2d=NULL; + + int numberoflayers; + int numareas=1; + + /* output: */ + int *int_element_partitioning = NULL; + int *int_node_partitioning = NULL; + double *element_partitioning = NULL; + double *node_partitioning = NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&MeshPartitionUsage); + + /*Fetch data: */ + FetchData(&dim,mxGetAssignedField(MODEL,0,"dimension")); + FetchData(&numberofelements,mxGetAssignedField(MODEL,0,"numberofelements")); + FetchData(&numberofvertices,mxGetAssignedField(MODEL,0,"numberofvertices")); + FetchData(&elements,NULL,&elements_width,mxGetAssignedField(MODEL,0,"elements")); + + if (dim==3){ + FetchData(&numberofelements2d,mxGetAssignedField(MODEL,0,"numberofelements2d")); + FetchData(&numberofvertices2d,mxGetAssignedField(MODEL,0,"numberofvertices2d")); + FetchData(&elements2d,NULL,NULL,mxGetAssignedField(MODEL,0,"elements2d")); + } + FetchData(&numberoflayers,mxGetAssignedField(MODEL,0,"numberoflayers")); + FetchData(&numareas,NUMAREAS); + + /*Run partitioning algorithm based on a "clever" use of the Metis partitioner: */ + MeshPartitionx(&int_element_partitioning,&int_node_partitioning,numberofelements,numberofvertices,elements, + numberofelements2d,numberofvertices2d,elements2d,numberoflayers,elements_width,dim,numareas); + + /*Post process node_partitioning and element_partitioning to be in double format. Metis needed them in int* format: */ + element_partitioning=(double*)xmalloc(numberofelements*sizeof(double)); + for (i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. + contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); + contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); + *(contours+i)=contouri; + } + + /* Debugging of contours :{{{1*/ + /*for(i=0;inods); + for (j=0;jnods;j++){ + printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); + } + }*/ + /*}}}*/ + + /*Run interpolation routine: */ + MeshProfileIntersectionx(&segments,&numsegs,index,x,y,nel,nods,contours,numcontours); + + /* output: */ + WriteData(SEGMENTS,segments,numsegs,5); + + /*end module: */ + MODULEEND(); + +} + +void MeshProfileIntersectionUsage(void){ + printf(" usage:\n"); + printf(" [segments]=MeshProfileIntersection(index,x,y,filename);\n"); + printf(" where:\n"); + printf(" input:\n"); + printf(" index,x,y is a triangulation\n"); + printf(" filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)\n"); + printf(" output:\n"); + printf(" segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremitis for a segment \n"); + printf(" belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the \n"); + printf(" mesh.\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/MeshProfileIntersection/MeshProfileIntersection.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/MeshProfileIntersection/MeshProfileIntersection.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/MeshProfileIntersection/MeshProfileIntersection.h (revision 12168) @@ -0,0 +1,38 @@ + +/* + MeshProfileIntersection.h +*/ + + +#ifndef _MESHPROFILEINTERSECTION_H +#define _MESHPROFILEINTERSECTION_H + +/* local prototypes: */ +void MeshProfileIntersectionUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "MeshProfileIntersection" + +/* input macros: */ +#define INDEX prhs[0] +#define X prhs[1] +#define Y prhs[2] +#define FILENAME prhs[3] + +/* serial output macros: */ +#define SEGMENTS (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 4 + +#endif /* _MESHPROFILEINTERSECTION_H */ + Index: /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 12168) @@ -0,0 +1,42 @@ +/*\file NodeConnectivity.c + *\brief: build node connectivity from elements. + */ + +#include "./NodeConnectivity.h" + +WRAPPER(NodeConnectivity){ + + /*inputs: */ + double* elements=NULL; + int nel; + int nods; + + /*outputs: */ + double* connectivity=NULL; + int width; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments: */ + CHECKARGUMENTS(NLHS,NRHS,&NodeConnectivityUsage); + + /*Input datasets: */ + FetchData(&elements,&nel,NULL,ELEMENTS); + FetchData(&nods,NUMNODES); + + /*!Generate internal degree of freedom numbers: */ + NodeConnectivityx(&connectivity, &width,elements,nel, nods); + + /*write output datasets: */ + WriteData(CONNECTIVITY,connectivity,nods,width); + + /*end module: */ + MODULEEND(); +} + +void NodeConnectivityUsage(void) { + _printf_(true,"\n"); + _printf_(true," usage: connectivity = %s(elements, numnodes);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/NodeConnectivity/NodeConnectivity.h (revision 12168) @@ -0,0 +1,58 @@ +/* + NodeConnectivity.h +*/ + +#ifndef _NODECONNECTIVITY_H +#define _NODECONNECTIVITY_H + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +/*Header files: */ +#include "../../c/include/globals.h" +#include "../../c/toolkits/toolkits.h" +#include "../../c/include/include.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" +#include "../../c/io/io.h" +#include "../../c/EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define ELEMENTS (mxArray*)prhs[0] +#define NUMNODES (mxArray*)prhs[1] +/* serial output macros: */ +#define CONNECTIVITY (mxArray**)&plhs[0] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define ELEMENTS PyTuple_GetItem(args,0) +#define NUMNODES PyTuple_GetItem(args,1) +/* serial output macros: */ +#define CONNECTIVITY output,0 +#endif + +#undef __FUNCT__ +#define __FUNCT__ "NodeConnectivity" + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 2 + +/* local prototypes: */ +void NodeConnectivityUsage(void); + +#endif /* _NODECONNECTIVITY_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 12168) @@ -0,0 +1,52 @@ +/*! \file PointCloudFindNeighbors + \brief: flag points that are too near one another, within an array of point coordinates +*/ + +#include "./PointCloudFindNeighbors.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + + int i,j; + + /* required input: */ + double* x=NULL; + double* y=NULL; + int nods; + double mindistance; + double multithread; + + /* output: */ + Vector* flags=NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&PointCloudFindNeighborsUsage); + + /*Fetch inputs: */ + FetchData(&x,&nods,NULL,XHANDLE); + FetchData(&y,NULL,NULL,YHANDLE); + FetchData(&mindistance,MINDISTANCE); + FetchData(&multithread,MULTITHREAD); + + /*Run core routine: */ + PointCloudFindNeighborsx(&flags,x,y,nods,mindistance,multithread); + + /* output: */ + WriteData(FLAGS,flags); + + /*end module: */ + MODULEEND(); +} + +void PointCloudFindNeighborsUsage(void){ + printf(" usage:\n"); + printf(" [flags]=PointCloudFindNeighbors(x,y,mindistance,multithread);\n\n"); + printf(" where:\n"); + printf(" x,y: list of points.\n"); + printf(" mindistance: minimum distance that should exist between points in the cloud.\n"); + printf(" multithread: run multithreaded or not. with multithreads, flags can get 1 and 2 values in duplicates.\n"); + printf(" flags: array of flags (flag==1 means point is within mindistance of another point)\n"); + printf("\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 12168) @@ -0,0 +1,44 @@ + +/* + PointCloudFindNeighbors.h +*/ + + +#ifndef _POINTCLOUDFINDNEIGHBORS_H +#define _POINTCLOUDFINDNEIGHBORS_H + +/* local prototypes: */ +void PointCloudFindNeighborsUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "PointCloudFindNeighbors" + + +#ifndef ALL +#define ALL 0 +#endif + +/* input macros: */ +#define XHANDLE prhs[0] +#define YHANDLE prhs[1] +#define MINDISTANCE prhs[2] +#define MULTITHREAD prhs[3] + +/* serial output macros: */ +#define FLAGS (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 4 + + +#endif /* _POINTCLOUDFINDNEIGHBORS_H */ + Index: /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp (revision 12168) @@ -0,0 +1,47 @@ +/*\file PropagateFlagsFromConnectivity.c + *\brief: propagate flags onto mesh, element by element, using connectivity. + */ + +#include "./PropagateFlagsFromConnectivity.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input/output datasets: */ + double* connectivity=NULL; + int nel; + double* pool=NULL; + double* flags=NULL; + int index; + int dummy; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&PropagateFlagsFromConnectivityUsage); + + /*Input datasets: */ + FetchData(&connectivity,&nel,&dummy,CONNECTIVITY); + FetchData(&pool,&dummy,POOL); + FetchData(&index,INDEX); + FetchData(&flags,&dummy,FLAGS); + + /*!Generate internal degree of freedom numbers: */ + PropagateFlagsFromConnectivityx(pool,connectivity,index,flags); + + /*write output datasets: */ + WriteData(POOLOUT,pool,nel); + + /*Free ressources: */ + xfree((void**)&connectivity); + xfree((void**)&flags); + + /*end module: */ + MODULEEND(); +} + +void PropagateFlagsFromConnectivityUsage(void) { + printf("\n"); + printf(" usage: [pool] = %s(connectivity,pool,index,flags);\n",__FUNCT__); + printf("\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 12168) @@ -0,0 +1,40 @@ + +/* + PropagateFlagsFromConnectivity.h +*/ + + +#ifndef _PROPAGATEFLAGSFROMCONNECTIVITY_H +#define _PROPAGATEFLAGSFROMCONNECTIVITY_H + +/* local prototypes: */ +void PropagateFlagsFromConnectivityUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "PropagateFlagsFromConnectivity" + +/* serial input macros: */ +#define CONNECTIVITY (mxArray*)prhs[0] +#define POOL (mxArray*)prhs[1] +#define INDEX (mxArray*)prhs[2] +#define FLAGS (mxArray*)prhs[3] + +/* serial output macros: */ +#define POOLOUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 4 + + +#endif /* _PROPAGATEFLAGSFROMCONNECTIVITY_H */ + + Index: /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.cpp (revision 12168) @@ -0,0 +1,267 @@ +/*\file Scotch.c + *\brief: Scotch partitioner mex module + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "./Scotch.h" + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + +#ifndef _HAVE_SCOTCH_ //only works if scotch library has been compiled in. + _error_(" Scotch not available! Cannot carry out Scotch partitioning!"); + #else + + int argcm; + char **argvm=NULL; + int nvert =0,nedge2=0,napar =0; + mwIndex *ir=NULL,*jc=NULL; + int *adjir=NULL,*adjjc=NULL; + double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; + int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; + char *archtyp=NULL; + int (*maptabi)[2]=NULL; + double* maptabd=NULL; + int i,j,k,imi=0,imo=0,isi=0,ierr; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + GmapUsage(); + return; + } + else if (nrhs < 6 || nlhs > 1) { + GmapUsage(); + mexErrMsgTxt(" "); + } + +/* load matlab argument list and convert to integer (note that converting here + and in the x-layer is inefficient, but it makes the x-layer more general) */ + + argvm = (char **) calloc(nrhs,sizeof(char *)); + + if (!(mxIsNumeric(prhs[imi]) && + (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { + argvm[isi] = (char *) calloc(4+1,sizeof(char)); + strcpy(argvm[isi],"gmap"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + __FUNCT__,argvm[isi]); + isi++; + } + else { + argvm[isi] = (char *) calloc(5+1,sizeof(char)); + strcpy(argvm[isi],"gpart"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + __FUNCT__,argvm[isi]); + isi++; + + argvm[isi] = (char *) calloc(17,sizeof(char)); + sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); + mexPrintf("%s -- Number of parts is %s.\n", + __FUNCT__,argvm[isi]); + isi++; + imi++; + } + + if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { + mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",__FUNCT__); + mexErrMsgTxt(" "); + } + else { + nvert =mxGetM(prhs[imi]); + nedge2=mxGetNzmax(prhs[imi]); + if (mxGetNzmax(prhs[imi])) { + ir =mxGetIr(prhs[imi]); + adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); + for (i=0; i= 5) && + (strncmp (argvm[0] + strlen (argvm[0]) - 5, "gpart", 5) == 0))) { + if (!mxIsChar(prhs[imi])) { + mexPrintf("%s -- Architecture type must be character.\n",__FUNCT__); + mexErrMsgTxt(" "); + } + else { + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); + mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); + } + mexPrintf("%s -- Architecture type is \"%s\".\n", + __FUNCT__,archtyp); + } + imi++; + + if (!mxIsNumeric(prhs[imi])) { + mexPrintf("%s -- Architecture parameter vector must be numeric.\n",__FUNCT__); + mexErrMsgTxt(" "); + } + else { + napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + apd=mxGetPr(prhs[imi]); + api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); + for (i=0; i=0; i--) + free(argvm[i]); + if (api) free(api); + if (archtyp) free(archtyp); + if (ewi) free(ewi); + if (vwi) free(vwi); + if (vli) free(vli); + if (adjjc) free(adjjc); + if (adjir) free(adjir);*/ + + return; +#endif //#ifndef _HAVE_SCOTCH_ +} + +void GmapUsage( void ) +{ + + mexPrintf("\n"); + mexPrintf("Usage: [maptab]=Scotch(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); + mexPrintf(" Scotch-specific parameters);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Scotch/Scotch.h (revision 12168) @@ -0,0 +1,40 @@ +/*!\file: Scotch.h + * \brief header file for Scotch module. + */ + +#ifndef _SCOTCH_H +#define _SCOTCH_H + +/* local prototypes: */ +void GmapUsage(void); + +#include +#include /* strcasecmp */ +#include /* clock,time,difftime */ + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Scotch" + +/* Scotch structures and prototypes */ +#ifdef MATLAB + #include "mat.h" + #include "mex.h" + #include "matrix.h" + + #define printf mexPrintf + #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) + #define malloc mxMalloc + #define calloc mxCalloc + #define realloc mxRealloc + #define free mxFree + #define exit(status) mexErrMsgTxt("exit=" #status) +#endif + + +#endif /* _SCOTCH_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.cpp (revision 12168) @@ -0,0 +1,100 @@ +/*\file Shp2Kml.c + *\brief: shp to kml file conversion mex module. + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./Shp2Kml.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + int i,verbose=1; + + /*input: */ + char *filshp=NULL,*filkml=NULL; + int sgn; + Options* options=NULL; + double cm=0.,sp=0.; + + /* output: */ + int iret=0; + + #ifndef _HAVE_SHAPELIB_ //only works if shapelib library has been compiled in. + _error_(" Shapelib not available! Cannot carry out shp file translation!"); + #endif + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { + Shp2KmlUsage(); _error_("Shp2Kml usage error"); + } + if (nrhs < NRHS) { + Shp2KmlUsage(); _error_("Shp2Kml usage error"); + } + + /*Input datasets: */ + FetchData(&filshp,SHP_IN); + FetchData(&filkml,KML_IN); + FetchData(&sgn,SGN_IN); + FetchData(&options,NRHS,nrhs,prhs); + + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); + if (verbose) printf(" sp=%g\n",sp); + } + + /*some checks*/ + if (sgn < -1 || sgn > +1) _error_("Hemisphere sgn=%d must be +1 (north), -1 (south), or 0 (no translation).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) + iret=Shp2Kmlx(filshp,filkml,sgn,cm,sp); + else + iret=Shp2Kmlx(filshp,filkml,sgn); + + /*Write data: */ + WriteData(RET_OUT,iret); + + /*Clean-up*/ + delete options; + xfree((void**)&filkml); + xfree((void**)&filshp); + + /*end module: */ + MODULEEND(); +} + +void Shp2KmlUsage(void){ + _printf_(true,"Shp2Kml - shp to kml file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from shp to kml format.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [ret]=Shp2Kml(filshp,filkml,sgn,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," filshp file name of shp file to be read (char, extension optional)\n"); + _printf_(true," filkml file name of kml file to be written (char)\n"); + _printf_(true," sgn sign for hemisphere (double, +1 (north); -1 (south); or 0 (no translation))\n"); + _printf_(true,"\n"); + _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); + _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); + _printf_(true,"\n"); + _printf_(true," ret return code (non-zero for warning)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [ret]=Shp2Kml('file.shp','file.kml', 0);\n"); + _printf_(true," [ret]=Shp2Kml('file.shp','file.kml', 1,'central_meridian',45,'standard_parallel',70);\n"); + _printf_(true," [ret]=Shp2Kml('file.shp','file.kml',-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Shp2Kml/Shp2Kml.h (revision 12168) @@ -0,0 +1,36 @@ +/*!\file Shp2Kml.h + * \brief: prototype for shp to kml file conversion mex module. + */ + +#ifndef _SHP2KML_H +#define _SHP2KML_H + +/* local prototypes: */ +void Shp2KmlUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Shp2Kml" + + +/* serial input macros: */ +#define SHP_IN prhs[0] +#define KML_IN prhs[1] +#define SGN_IN prhs[2] + +/* serial output macros: */ +#define RET_OUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 3 +#undef NLHS +#define NLHS 1 + +#endif + Index: /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.cpp (revision 12168) @@ -0,0 +1,32 @@ +/*\file StringToEnum.c + *\brief:convert enum (int) to string + */ + +#include "./StringToEnum.h" + +void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + char *name = NULL; + int enum_out; + + /*checks on arguments on the matlab side: */ + if(nrhs!=NRHS){ + StringToEnumUsage(); _error_(" usage. See above"); + } + + /*Fetch inputs: */ + FetchData(&name,NAME); + + /*Run core function: */ + enum_out=StringToEnumx(name); + + /* output: */ + WriteData(ENUMOUT,enum_out); +} + +void StringToEnumUsage(void) +{ + _printf_(true,"\n"); + _printf_(true," usage: %senum = StringToEnum(string);\n",__FUNCT__); + _printf_(true,"\n"); +} Index: /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/StringToEnum/StringToEnum.h (revision 12168) @@ -0,0 +1,32 @@ +/*!\file: StringToEnum.h + * \brief header file for StringToEnum module. + */ + +#ifndef _STRINGTOENUM_H +#define _STRINGTOENUM_H + +/* local prototypes: */ +void StringToEnumUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +/* serial input macros: */ +#define NAME (mxArray*)prhs[0] + +/* serial output macros: */ +#define ENUMOUT (mxArray**)&plhs[0] + +/* serial arg counts: */ +#undef NLHS +#define NLHS 1 +#undef NRHS +#define NRHS 1 + +#undef __FUNCT__ +#define __FUNCT__ "StringToEnum" + +#endif /* _TEST_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.cpp (revision 12168) @@ -0,0 +1,73 @@ +/* + * TriMesh: mesh a domain using an .exp file + */ + +#include "./TriMesh.h" + +WRAPPER(TriMesh){ + + /* input: */ + char *domainname = NULL; + char *riftsname = NULL; + double area; + + /*intermediary: */ + DataSet *domain = NULL; + DataSet *rifts = NULL; + + /* output: */ + Matrix *index = NULL; + Vector *x = NULL; + Vector *y = NULL; + Matrix *segments = NULL; + Vector *segmentmarkerlist = NULL; + + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments: */ + CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage); + + /*Fetch data needed for meshing: */ + FetchData(&domainname,DOMAINOUTLINE); + FetchData(&riftsname,RIFTSOUTLINE); + FetchData(&area,AREA); + + /*Read domain outline: */ + domain = DomainOutlineRead(domainname); + rifts = DomainOutlineRead(riftsname); + + /*call x core: */ + TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,rifts,area); + + /*write outputs: */ + WriteData(INDEX,index); + WriteData(X,x); + WriteData(Y,y); + WriteData(SEGMENTS,segments); + WriteData(SEGMENTMARKERLIST,segmentmarkerlist); + + /*free ressources: */ + delete domain; + delete rifts; + xdelete_module(&index); + xdelete_module(&x); + xdelete_module(&y); + xdelete_module(&segments); + xdelete_module(&segmentmarkerlist); + + /*end module: */ + MODULEEND(); +} + +void TriMeshUsage(void) //{{{1 +{ + printf("\n"); + printf(" usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,rifts,area) \n"); + printf(" where: index,x,y defines a triangulation, segments is an array made \n"); + printf(" of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n"); + printf(" outlinefilename an Argus domain outline file, \n"); + printf(" area is the maximum area desired for any element of the resulting mesh, \n"); + printf("\n"); +} +//}}} Index: /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/TriMesh/TriMesh.h (revision 12168) @@ -0,0 +1,68 @@ +/* + TriMesh.h +*/ + +#ifndef _TRIMESH_H +#define _TRIMESH_H + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ +#ifdef _HAVE_PYTHON_ +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#endif + +/*Header files: */ +#include "../../c/include/globals.h" +#include "../../c/toolkits/toolkits.h" +#include "../../c/include/include.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" +#include "../../c/io/io.h" +#include "../../c/EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_MATLAB_MODULES_ +/* serial input macros: */ +#define DOMAINOUTLINE (mxArray *)prhs[0] +#define RIFTSOUTLINE (mxArray *)prhs[1] +#define AREA (mxArray *)prhs[2] +/* serial output macros: */ +#define INDEX (mxArray**)&plhs[0] +#define X (mxArray**)&plhs[1] +#define Y (mxArray**)&plhs[2] +#define SEGMENTS (mxArray**)&plhs[3] +#define SEGMENTMARKERLIST (mxArray**)&plhs[4] +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +/* serial input macros: */ +#define DOMAINOUTLINE PyTuple_GetItem(args,0) +#define RIFTSOUTLINE PyTuple_GetItem(args,1) +#define AREA PyTuple_GetItem(args,2) +/* serial output macros: */ +#define INDEX output,0 +#define X output,1 +#define Y output,2 +#define SEGMENTS output,3 +#define SEGMENTMARKERLIST output,4 +#endif + +#undef __FUNCT__ +#define __FUNCT__ "TriMesh" + +/* serial arg counts: */ +#undef NLHS +#define NLHS 5 +#undef NRHS +#define NRHS 3 + +/* local prototypes: */ +void TriMeshUsage(void); + +#endif /* _TRIMESH_H */ Index: /issm/branches/trunk-jpl-damage/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 12168) @@ -0,0 +1,331 @@ +/*!\file: TriMeshProcessRifts.cpp + * \brief split a mesh where a rift (or fault) is present + */ + +#include "./TriMeshProcessRifts.h" + +void mexFunction( int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[] ) { + + + /*Matlab arrays: */ + mxArray* pmxa_array=NULL; + mxArray* pmxa_array2=NULL; + mxArray* pmxa_array3=NULL; + int i,j,k,counter; + + /* returned quantities: */ + int out_numrifts; + int* out_riftsnumsegments=NULL; + double** out_riftssegments=NULL; + int* out_riftsnumpairs=NULL; + double** out_riftspairs=NULL; + double* out_riftstips=NULL; + double** out_riftspenaltypairs=NULL; + int* out_riftsnumpenaltypairs=NULL; + + /*empty rifts structure: */ + double* pNaN=NULL; + const char* fnames[10]; + mwSize ndim=2; + mwSize dimensions[2] = {1,1}; + double* pair=NULL; + + + /* input: */ + double* tindex_in=NULL; + double* index_in=NULL; + int nel; + double* x_inm=NULL; //matlab vector + double* x_in=NULL; //copy of matlab vector + int nods; + double* y_inm=NULL;//matlab vector + double* y_in=NULL;//copy of matlab vector + double* tsegments_in=NULL; + double* segments_in=NULL; + double* tsegmentmarkers_in=NULL; + double* segmentmarkers_in=NULL; + + /* state: */ + double* state=NULL; + + int num_seg; + + /*rifts: */ + int riftflag; + int numrifts; + + /* verify correct usage: */ + if (nlhs==0 && nrhs==0) { + /* special case: */ + TriMeshProcessRiftsUsage(); + return; + } + + if (!( (nlhs==6) || (nrhs==5))){ + mexPrintf(" %s format error.\n", __FUNCT__); + TriMeshProcessRiftsUsage(); + printf(" "); + mexErrMsgTxt(" "); + } + + /*Fetch index_in: */ + if(mxIsDouble(prhs[0])){ + nel=mxGetM(prhs[0]); + tindex_in=mxGetPr(prhs[0]); + index_in=(double*)xmalloc(nel*3*sizeof(double)); + for (i=0;i NLHS) { + Xy2llUsage(); _error_("Xy2ll usage error"); + } + if (nrhs < NRHS) { + Xy2llUsage(); _error_("Xy2ll usage error"); + } + + /*Input datasets: */ + FetchData(&x,&nx,X_IN); + FetchData(&y,&ny,Y_IN); + FetchData(&sgn,SGN_IN); + FetchData(&options,NRHS,nrhs,prhs); + + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); + if (verbose) printf(" sp=%g\n",sp); + } + + /*some checks*/ + if (nx != ny) _error_("Must have same number of x[%d] and y[%d] coordinates.",nx,ny); + else ncoord=nx; + if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + lat=(double*)mxMalloc(ncoord*sizeof(double)); + lon=(double*)mxMalloc(ncoord*sizeof(double)); + + /* Run core computations: */ + if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) + iret=Xy2llx(lat,lon,x,y,ncoord,sgn,cm,sp); + else + iret=Xy2llx(lat,lon,x,y,ncoord,sgn); + + /*Write data: */ + WriteData(LAT_OUT,lat,ncoord); + WriteData(LON_OUT,lon,ncoord); + + /*Clean-up*/ + delete options; + + /*end module: */ + MODULEEND(); +} + +void Xy2llUsage(void){ + _printf_(true,"Xy2ll - x/y to lat/long coordinate transformation module:\n"); + _printf_(true,"\n"); + _printf_(true," This module transforms x/y to lat/long coordinates.\n"); + _printf_(true,"\n"); + _printf_(true," Usage:\n"); + _printf_(true," [lat,lon]=Xy2ll(x,y,sgn,'param name',param,...);\n"); + _printf_(true,"\n"); + _printf_(true," x x coordinates (double vector)\n"); + _printf_(true," y y coordinates (double vector)\n"); + _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); + _printf_(true,"\n"); + _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); + _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); + _printf_(true,"\n"); + _printf_(true," lat latitude coordinates (double vector)\n"); + _printf_(true," lon longitude coordinates (double vector)\n"); + _printf_(true,"\n"); + _printf_(true," Examples:\n"); + _printf_(true," [lat,lon]=Xy2ll(x,y, 1);\n"); + _printf_(true," [lat,lon]=Xy2ll(x,y, 1,'central_meridian',45,'standard_parallel',70);\n"); + _printf_(true," [lat,lon]=Xy2ll(x,y,-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); +} + Index: /issm/branches/trunk-jpl-damage/src/modules/Xy2ll/Xy2ll.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Xy2ll/Xy2ll.h (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/Xy2ll/Xy2ll.h (revision 12168) @@ -0,0 +1,37 @@ +/*!\file Xy2ll.h + * \brief: prototype for x/y to lat/long coordinate mex module. + */ + +#ifndef _XY2LL_H +#define _XY2LL_H + +/* local prototypes: */ +void Xy2llUsage(void); + +#include "../../c/include/globals.h" +#include "../../c/modules/modules.h" +#include "../../c/Container/Container.h" +#include "../../c/shared/shared.h" +#include "../../c/issm-binding.h" + +#undef __FUNCT__ +#define __FUNCT__ "Xy2ll" + + +/* serial input macros: */ +#define X_IN prhs[0] +#define Y_IN prhs[1] +#define SGN_IN prhs[2] + +/* serial output macros: */ +#define LAT_OUT (mxArray**)&plhs[0] +#define LON_OUT (mxArray**)&plhs[1] + +/* serial arg counts: */ +#undef NRHS +#define NRHS 3 +#undef NLHS +#define NLHS 2 + +#endif + Index: /issm/branches/trunk-jpl-damage/src/modules/matlab/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/matlab/Makefile.am (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/matlab/Makefile.am (revision 12168) @@ -0,0 +1,163 @@ +INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ +EXEEXT=$(MATLABWRAPPEREXT) +#Bin programs {{{1 +if MODULES +bin_PROGRAMS = AverageFilter\ + BamgMesher\ + BamgConvertMesh\ + BamgTriangulate\ + Chaco\ + ContourToMesh \ + ContourToNodes \ + ElementConnectivity\ + EnumToString\ + Exp2Kml \ + HoleFiller \ + InternalFront\ + InterpFromGridToMesh \ + InterpFromMeshToMesh2d \ + InterpFromMeshToMesh3d \ + InterpFromMeshToGrid \ + InterpFromMesh2d \ + KMLFileRead \ + KMLMeshWrite \ + KMLOverlay \ + Kml2Exp \ + Kriging \ + Ll2xy \ + NodeConnectivity \ + MeshPartition\ + MeshProfileIntersection\ + PointCloudFindNeighbors\ + PropagateFlagsFromConnectivity\ + Scotch\ + Shp2Kml\ + StringToEnum\ + TriaSearch\ + TriMesh\ + TriMeshProcessRifts\ + Xy2ll +endif +#}}} +#Flags and libraries {{{1 +LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) + +#Triangle library +AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER + +#Matlab part +AM_LDFLAGS = $(MEXLINK) +AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread +LDADD += $(MEXLIB) ../../c/libISSMMatlab.a + +LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a + +#Optimization flags: +AM_CXXFLAGS += $(CXXOPTFLAGS) +#}}} +#Bin sources {{{1 +AverageFilter_SOURCES = ../AverageFilter/AverageFilter.cpp\ + ../AverageFilter/AverageFilter.h + +BamgMesher_SOURCES = ../BamgMesher/BamgMesher.cpp\ + ../BamgMesher/BamgMesher.h + +BamgConvertMesh_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\ + ../BamgConvertMesh/BamgConvertMesh.h + +BamgTriangulate_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\ + ../BamgTriangulate/BamgTriangulate.h + +Chaco_SOURCES = ../Chaco/Chaco.cpp\ + ../Chaco/Chaco.h + +ContourToMesh_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ + ../ContourToMesh/ContourToMesh.h + +ContourToNodes_SOURCES = ../ContourToNodes/ContourToNodes.cpp\ + ../ContourToNodes/ContourToNodes.h + +ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ + ../ElementConnectivity/ElementConnectivity.h + +EnumToString_SOURCES = ../EnumToString/EnumToString.cpp\ + ../EnumToString/EnumToString.h + +StringToEnum_SOURCES = ../StringToEnum/StringToEnum.cpp\ + ../StringToEnum/StringToEnum.h + +HoleFiller_SOURCES = ../HoleFiller/HoleFiller.cpp\ + ../HoleFiller/HoleFiller.h + +InternalFront_SOURCES = ../InternalFront/InternalFront.cpp\ + ../InternalFront/InternalFront.h + +InterpFromGridToMesh_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\ + ../InterpFromGridToMesh/InterpFromGridToMesh.h + +InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ + ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h + +InterpFromMeshToMesh3d_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\ + ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h + +InterpFromMeshToGrid_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\ + ../InterpFromMeshToGrid/InterpFromMeshToGrid.h + +InterpFromMesh2d_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\ + ../InterpFromMesh2d/InterpFromMesh2d.h + +KMLFileRead_SOURCES = ../KMLFileRead/KMLFileRead.cpp\ + ../KMLFileRead/KMLFileRead.h + +KMLMeshWrite_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\ + ../KMLMeshWrite/KMLMeshWrite.h + +KMLOverlay_SOURCES = ../KMLOverlay/KMLOverlay.cpp\ + ../KMLOverlay/KMLOverlay.h + +Xy2ll_SOURCES = ../Xy2ll/Xy2ll.cpp\ + ../Xy2ll/Xy2ll.h + +Ll2xy_SOURCES = ../Ll2xy/Ll2xy.cpp\ + ../Ll2xy/Ll2xy.h + +Exp2Kml_SOURCES = ../Exp2Kml/Exp2Kml.cpp\ + ../Exp2Kml/Exp2Kml.h + +Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\ + ../Kml2Exp/Kml2Exp.h + +Kriging_SOURCES = ../Kriging/Kriging.cpp\ + ../Kriging/Kriging.h + +MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\ + ../MeshPartition/MeshPartition.h + +MeshProfileIntersection_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\ + ../MeshProfileIntersection/MeshProfileIntersection.h + +NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ + ../NodeConnectivity/NodeConnectivity.h + +PointCloudFindNeighbors_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ + ../PointCloudFindNeighbors/PointCloudFindNeighbors.h + +PropagateFlagsFromConnectivity_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\ + ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h + +Scotch_SOURCES = ../Scotch/Scotch.cpp\ + ../Scotch/Scotch.h + +Shp2Kml_SOURCES = ../Shp2Kml/Shp2Kml.cpp\ + ../Shp2Kml/Shp2Kml.h + +TriaSearch_SOURCES = ../TriaSearch/TriaSearch.cpp\ + ../TriaSearch/TriaSearch.h + +TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h + +TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\ + ../TriMeshProcessRifts/TriMeshProcessRifts.h +#}}} Index: /issm/branches/trunk-jpl-damage/src/modules/python/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/python/Makefile.am (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/modules/python/Makefile.am (revision 12168) @@ -0,0 +1,42 @@ +INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ +EXEEXT=$(PYTHONWRAPPEREXT) +#Bin programs {{{1 +if MODULES +bin_PROGRAMS = ElementConnectivity\ + InterpFromMeshToMesh2d \ + NodeConnectivity\ + TriMesh +endif +#}}} +#Flags and libraries {{{1 +LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) + +#Triangle library +AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER + +#Python part +AM_LDFLAGS = $(PYTHONLINK) +AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ +if PYTHON3 +AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API +endif +LDADD += $(BOOSTLIB) $(PYTHONLIB) ../../c/libISSMPython.a + +LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a + +#Optimization flags: +AM_CXXFLAGS += $(CXXOPTFLAGS) +#}}} +#Bin sources {{{1 +ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ + ../ElementConnectivity/ElementConnectivity.h + +InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ + ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h + +NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ + ../NodeConnectivity/NodeConnectivity.h + +TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h +#}}} Index: /issm/branches/trunk-jpl-damage/src/py/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/py/Makefile.am (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/py/Makefile.am (revision 12168) @@ -0,0 +1,1 @@ +SUBDIRS = model Index: /issm/branches/trunk-jpl-damage/src/py/model/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/py/model/Makefile.am (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/py/model/Makefile.am (revision 12168) @@ -0,0 +1,11 @@ +bin_SCRIPTS = petscversion.py +CLEANFILES = $(bin_SCRIPTS) + +if PYTHON3 +%.py : %.2.py + cp -f $< $@ + 2to3 -n -w $@ +else +%.py : %.2.py + ln -s -f $< $@ +endif Index: sm/branches/trunk-jpl-damage/src/py/model/display/fielddisplay.rest =================================================================== --- /issm/branches/trunk-jpl-damage/src/py/model/display/fielddisplay.rest (revision 12167) +++ (revision ) @@ -1,154 +1,0 @@ -def fielddisplay(md,name,comment): -#FIELDDISPLAY - display model field -# -# Usage: -# fielddisplay(md,offset,name,comment) - - #get field - field=getattr(md,name) - - #disp corresponding line as a function of field type (offset set as 9 spaces) - #parsedisplay(' ',name,field,comment); - - return - -function parsedisplay(offset,name,field,comment); %{{{ - - %string - if ischar(field), - - if length(field)>30; - displayunit(offset,name,'not displayed',comment), - else - displayunit(offset,name,['''' field ''''],comment), - end - - %numeric - elseif isnumeric(field) - - %get size - fieldsize=size(field); - - %double - if max(fieldsize)==1, - displayunit(offset,name,num2str(field),comment), - %matrix - else - displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), - end - - %logical - elseif islogical(field) - - %get size - fieldsize=size(field); - - %single value - if max(fieldsize)==1, - if (field) - displayunit(offset,name,'true',comment), - else - displayunit(offset,name,'false',comment), - end - %matrix - else - displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), - end - - %structure - elseif isstruct(field), - if ~isempty(fields(field)) - displayunit(offset,name,'(structure)',comment), - struct_display(field,[offset ' ']), - else - displayunit(offset,name,'N/A',comment), - end - - %cell - elseif iscell(field), - cell_display(offset,name,field,comment), - - else - displayunit(offset,name,'not displayed',comment), - - end -end%}}} - -function struct_display(structure,offset) % {{{ - - structure_fields=fields(structure); - - for i=1:length(structure_fields), - - %get current field - field=structure.(structure_fields{i}); - - %recursive call if necessary - if isstruct(field), - displayunit(offset,structure_fields{i},'(structure)',''), - struct_display(field,[offset ' ']); - - %display value - else - parsedisplay(offset,structure_fields{i},field,''); - end - end -end% }}} -function cell_display(offset,name,field,comment) % {{{ - - %initialization - string='{'; - - %go through the cell and fill string - if length(field)<5; - for i=1:length(field), - if ischar(field{i}), - string=[string '''' field{i} ''',']; - elseif (isnumeric(field{i}) & length(field{i})==1) - string=[string num2str(field{i}) ',' ]; - else - string='{'; - break - end - end - end - if strcmp(string,'{'), - string=['(' num2str(size(field,1)) 'x' num2str(size(field,2)) ')']; - else - string=[string(1:end-1) '}']; - end - - %call displayunit - displayunit(offset,name,string,comment); -end% }}} -function displayunit(offset,name,characterization,comment),% {{{ - - %take care of name - if length(name)>23, - name=[name(1:20) '...']; - end - - %take care of characterization - if (strcmp(characterization,['''' '''']) | strcmp(characterization,'NaN')), - characterization='N/A'; - end - if length(characterization)>15, - characterization=[characterization(1:12) '...']; - end - - %print - if isempty(comment) - disp(sprintf('%s%-23s: %-15s',offset,name,characterization)); - else - if ischar(comment), - disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment)); - elseif iscell(comment), - disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment{1})); - for i=2:length(comment), - disp(sprintf('%s%-23s %-15s %s',offset,'','',comment{i})); - end - else - error('fielddisplay error message: format for comment not supportet yet'); - end - end -end% }}} Index: /issm/branches/trunk-jpl-damage/src/py/model/petscversion.2.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/py/model/petscversion.2.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/src/py/model/petscversion.2.py (revision 12168) @@ -0,0 +1,39 @@ +#PETSCVERSION - recover petsc version number, inside config.h file +# +# Usage: +# PETSC_VERSION=petscversion(); + +#Module imports {{{ +import os +import sys +from issmtier import * +#}}} + +def petscversion(): + + #default + PETSC_VERSION=3; + + configfile=issmtier() + "/bin/config.h" #should find it in the install target + + if not os.path.isfile(configfile): + raise RuntimeError("%s%s%s"%("File ",configfile," not found. ISSM has not been configured yet!")) + + #go through the file, and recover the line we want + fid=open(configfile,'r'); + + tline=fid.readline() + while tline: + + if tline=='': + break + + if tline[0:21]=="#define _PETSC_MAJOR_": + PETSC_VERSION=int(tline[22]) + break + + tline=fid.readline() + + fid.close(); + + return PETSC_VERSION Index: sm/branches/trunk-jpl-damage/src/py/model/petscversion.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/py/model/petscversion.py (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -#PETSCVERSION - recover petsc version number, inside config.h file -# -# Usage: -# PETSC_VERSION=petscversion(); - -#Module imports {{{ -import os -import sys -from issmtier import * -#}}} - -def petscversion(): - - #default - PETSC_VERSION=3; - - configfile=issmtier() + "/bin/config.h" #should find it in the install target - - if not os.path.isfile(configfile): - raise RuntimeError("%s%s%s"%("File ",configfile," not found. ISSM has not been configured yet!")) - - #go through the file, and recover the line we want - fid=open(configfile,'r'); - - tline=fid.readline() - while tline: - - if tline=='': - break - - if tline[0:21]=="#define _PETSC_MAJOR_": - PETSC_VERSION=int(tline[22]) - break - - tline=fid.readline() - - fid.close(); - - return PETSC_VERSION Index: /issm/branches/trunk-jpl-damage/startup.m =================================================================== --- /issm/branches/trunk-jpl-damage/startup.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/startup.m (revision 12168) @@ -11,35 +11,35 @@ lastwarn(''); -%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN +%Recover ISSM_DIR , or if on a Windows machine, ISSM_DIR_WIN if ~ispc, - ISSM_TIER=getenv('ISSM_TIER'); + ISSM_DIR=getenv('ISSM_DIR'); else - ISSM_TIER=getenv('ISSM_TIER_WIN'); - %ISSM_TIER=''; + ISSM_DIR=getenv('ISSM_DIR_WIN'); + %ISSM_DIR=''; end -if (isempty(ISSM_TIER)), - error('''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); +if (isempty(ISSM_DIR)), + error('''ISSM_DIR'' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!'); end %Now add all issm code paths necessary to run issm smoothly. %We capture the error output, so that we can warn the user to update -%the variable ISSM_TIER in this file, in case it is not correctly setup. +%the variable ISSM_DIR in this file, in case it is not correctly setup. %ISSM path -addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath -addpath([ISSM_TIER '/bin']); -addpath(recursivepath([ISSM_TIER '/src/m'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/scotch'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/canos'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/kml'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/export_fig'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/googleearthtoolbox'])); -addpath(recursivepath([ISSM_TIER '/externalpackages/cm_and_cb_utilities'])); +addpath([ISSM_DIR '/src/m/utils/']); %loads recursivepath +addpath([ISSM_DIR '/bin']); +addpath(recursivepath([ISSM_DIR '/src/m'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/scotch'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/canos'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/kml'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/export_fig'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/googleearthtoolbox'])); +addpath(recursivepath([ISSM_DIR '/externalpackages/cm_and_cb_utilities'])); -clear ISSM_TIER; +clear ISSM_DIR; %Check on any warning messages that might indicate that the paths were not correct. if ~isempty(lastwarn), - fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); + fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_DIR variable in your .cshrc or .bashrc!\n'); fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); else Index: /issm/branches/trunk-jpl-damage/startup.py =================================================================== --- /issm/branches/trunk-jpl-damage/startup.py (revision 12167) +++ /issm/branches/trunk-jpl-damage/startup.py (revision 12168) @@ -5,27 +5,30 @@ # before handing over the prompt to the user if the environment variable # PYTHONSTARTUP is defined: -# export PYTHONSTARTUP=$ISSM_TIER/startup.py +# export PYTHONSTARTUP=$ISSM_DIR/startup.py # This startup script should be run by users before trying to use ISSM. import os,sys - -#First check we are running python 3 at least -if sys.version_info[0] < 3: - print("ISSM can only work in Python 3. Exiting python") - sys.exit(1) - -#Recover ISSM_TIER, ISSM_DIR and USERNAME -ISSM_TIER=os.getenv('ISSM_TIER') +#Recover ISSM_DIR and USERNAME +ISSM_DIR=os.getenv('ISSM_DIR') USERNAME =os.getenv('USER') -if(ISSM_TIER==None): - raise NameError('"ISSM_TIER" environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!') +if(ISSM_DIR==None): + raise NameError('"ISSM_DIR" environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!') #Now add all issm code paths necessary to run issm smoothly. #We capture the error output, so that we can warn the user to update -#the variable ISSM_TIER in this file, in case it is not correctly setup. +#the variable ISSM_DIR in this file, in case it is not correctly setup. #ISSM path. Go through src/py and load everything we find that looks like a python file -for root,dirs,files in os.walk(ISSM_TIER+ '/src/py'): +for root,dirs,files in os.walk(ISSM_DIR+ '/src/py'): + for file in files: + if file.find(".py") != -1: + if file.find(".pyc") == -1: + #add to path + sys.path.append(root) + file=os.path.splitext(file)[0] + #__import__(file) + +for root,dirs,files in os.walk(ISSM_DIR+ '/src/m'): for file in files: if file.find(".py") != -1: @@ -36,5 +39,5 @@ #__import__(file) -sys.path.append(ISSM_TIER + '/src/mex') +sys.path.append(ISSM_DIR + '/src/modules/python') #Deal with scipy import: @@ -79,5 +82,6 @@ from miscellaneous import * from private import * -from TriMesh import * +from triangle import * +from setmask import * #}}} Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m (revision 12168) @@ -30,6 +30,6 @@ % md=runme('id',102,'procedure','model'); -%Get ISSM_TIER variable -ISSM_TIER=issmtier(); +%Get ISSM_DIR variable +ISSM_DIR=issmdir(); %Check inputs @@ -168,5 +168,5 @@ message=getReport(me2); if strcmpi(output,'nightly') - fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at'); fprintf(fid,'%s',message); fprintf(fid,'\n------------------------------------------------------------------\n'); @@ -174,5 +174,5 @@ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); elseif strcmpi(output,'daily'); - fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); fprintf(fid,'%s',message); fprintf(fid,'\n------------------------------------------------------------------\n'); @@ -193,5 +193,5 @@ message=getReport(me); if strcmpi(output,'nightly') - fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at'); fprintf(fid,'%s',message); fprintf(fid,'\n------------------------------------------------------------------\n'); @@ -199,5 +199,5 @@ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); elseif strcmpi(output,'daily'); - fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); + fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); fprintf(fid,'%s',message); fprintf(fid,'\n------------------------------------------------------------------\n'); Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test101.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test101.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test101.py =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test101.py (revision 12167) +++ (revision ) @@ -1,6 +1,0 @@ -from model import * -from TriMesh import * - -md=model() -[a,b,c,d,e]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) -print(a,b,c,d,e) Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test102.py =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test102.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test102.py (revision 12168) @@ -0,0 +1,9 @@ +from model import * +from triangle import * +from setmask import * +from parameterize import * + +md=model(); +md=triangle(md,'../Exp/Square.exp',50000); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareShelfConstrained.py') Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test103.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test103.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,2); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test105.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test105.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test107.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test107.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,2); -md.cluster=none; -md=setflowequation(md,'stokes','all'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test109.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test109.m (revision 12167) +++ (revision ) @@ -1,13 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test111.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test111.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=meshconvert(md); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.geometry.thickness; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test113.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test113.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md=extrude(md,5,3); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test115.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test115.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.timestepping.time_step=0; -md.cluster=none; -md=solve(md,ThermalSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.ThermalSolution.Temperature),... - (md.results.ThermalSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test117.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test117.m (revision 12167) +++ (revision ) @@ -1,19 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test119.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test119.m (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - - - - - - - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test121.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test121.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test123.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test123.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,SurfaceSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... - (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test125.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test125.m (revision 12167) +++ (revision ) @@ -1,15 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,5,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,SurfaceSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... - (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test127.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test127.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BedSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'BedSlopeX','BedSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.BedSlopeSolution.BedSlopeX),... - (md.results.BedSlopeSolution.BedSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test129.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test129.m (revision 12167) +++ (revision ) @@ -1,15 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,5,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BedSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'BedSlopeX','BedSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.BedSlopeSolution.BedSlopeX),... - (md.results.BedSlopeSolution.BedSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test131.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test131.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -%Add boundary conditions on thickness on the border -pos=find(md.mesh.vertexonboundary); -md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test133.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test133.m (revision 12167) +++ (revision ) @@ -1,17 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,5,1); -%Add boundary conditions on thickness on the border -pos=find(md.mesh.vertexonboundary); -md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test135.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test135.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=meshconvert(md); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md.balancethickness.stabilization=3; -md.initialization.vy=md.initialization.vy+400; -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test137.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test137.m (revision 12167) +++ (revision ) @@ -1,25 +1,0 @@ - -%Simple mesh -md=bamg(model,'domain','../Exp/Square.exp','hmax',100000); -x1=md.mesh.x; -y1=md.mesh.y; - -%hVertices -md=bamg(model,'domain','../Exp/Square.exp','hmax',300000,'hvertices',[10000 100000 400000 100000]'); -x2=md.mesh.x; -y2=md.mesh.y; - -%big mesh -t0=clock; -md=bamg(model,'domain','../Exp/Square.exp','hmax',3000); -nbelements=md.mesh.numberofelements; -elapsedtime=etime(clock,t0); - -%Fields and tolerances to track changes -field_names ={'x1' 'y1' 'x2' 'y2' 'nbelements' 'elapsed time'}; -field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 0.5}; -field_values={... - x1, y1,... - x2, y2,... - nbelements,elapsedtime... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test139.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test139.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.timestepping.time_step=0; -md.cluster=none; -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md=solve(md,EnthalpySolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Enthalpy','Waterfraction','Temperature'}; -field_tolerances={1e-13,1e-10,1e-13}; -field_values={... - (md.results.EnthalpySolution.Enthalpy),... - (md.results.EnthalpySolution.Waterfraction),... - (md.results.EnthalpySolution.Temperature),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test141.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test141.m (revision 12167) +++ (revision ) @@ -1,30 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md.thermal.isenthalpy=1; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Enthalpy1','Waterfraction1','Temperature1',... - 'Enthalpy2','Waterfraction2','Temperature2',... - 'Enthalpy3','Waterfraction3','Temperature3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Enthalpy),... - (md.results.TransientSolution(1).Waterfraction),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(2).Enthalpy),... - (md.results.TransientSolution(2).Waterfraction),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(3).Enthalpy),... - (md.results.TransientSolution(3).Waterfraction),... - (md.results.TransientSolution(3).Temperature),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test143.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test143.m (revision 12167) +++ (revision ) @@ -1,53 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md.thermal.isenthalpy=1; -md.thermal.stabilization=2; -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).Enthalpy),... - (md.results.TransientSolution(1).Waterfraction),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).Enthalpy),... - (md.results.TransientSolution(2).Waterfraction),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).Enthalpy),... - (md.results.TransientSolution(3).Waterfraction),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test201.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test201.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test203.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test203.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test205.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test205.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test207.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test207.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,2); -md.cluster=none; -md=setflowequation(md,'stokes','all'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test209.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test209.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test211.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test211.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.timestepping.time_step=0; -md.cluster=none; -md=solve(md,ThermalSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.ThermalSolution.Temperature),... - (md.results.ThermalSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test213.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test213.m (revision 12167) +++ (revision ) @@ -1,23 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature1','MeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test215.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test215.m (revision 12167) +++ (revision ) @@ -1,33 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test217.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test217.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test219.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test219.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test221.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test221.m (revision 12167) +++ (revision ) @@ -1,48 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); -md.diagnostic.reltol=NaN; -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... - 1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... - 1e-08,1e-08,1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test223.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test223.m (revision 12167) +++ (revision ) @@ -1,33 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'MaterialsRheologyBbar'}; -md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.MaterialsRheologyBbar),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test225.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test225.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'MaterialsRheologyBbar'}; -md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.MaterialsRheologyB),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test227.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test227.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'MaterialsRheologyBbar'}; -md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.MaterialsRheologyB),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test229.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test229.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'MaterialsRheologyBbar'}; -md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.MaterialsRheologyB),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test233.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test233.m (revision 12167) +++ (revision ) @@ -1,69 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%redo the parameter file for this special shelf. -%constant thickness, constrained (vy=0) flow into an icefront, -%from 0 m/yr at the grounding line. - -%tighten -md.diagnostic.restol=10^-4; - -%needed later -ymin=min(md.mesh.y); -ymax=max(md.mesh.y); -xmin=min(md.mesh.x); -xmax=max(md.mesh.x); - -di=md.materials.rho_ice/md.materials.rho_water; - -h=1000; -md.geometry.thickness=h*ones(md.mesh.numberofvertices,1); -md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; - -%Initial velocity and pressure -md.initialization.vx=zeros(md.mesh.numberofvertices,1); -md.initialization.vy=zeros(md.mesh.numberofvertices,1); -md.initialization.vz=zeros(md.mesh.numberofvertices,1); -md.initialization.pressure=zeros(md.mesh.numberofvertices,1); - -%Materials -md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); -md.materials.rheology_B=paterson(md.initialization.temperature); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); - -%Boundary conditions: -md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); -md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); -md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - -%constrain flanks to 0 normal velocity -pos=find(md.mesh.x==xmin | md.mesh.x==xmax); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvz(pos)=NaN; - -%constrain grounding line to 0 velocity -pos=find(md.mesh.y==ymin); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; - -%icefront -nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; -pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); -diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; -md.diagnostic.icefront=diagnostic.icefront; - -md=solve(md,DiagnosticSolutionEnum); - -%create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. -%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; -%vy_c=ey_c.*md.mesh.y*md.constants.yts; - -%Fields and tolerances to track changes -field_names ={'Vy'}; -field_tolerances={1e-13}; -field_values={(md.results.DiagnosticSolution.Vy)}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test235.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test235.m (revision 12167) +++ (revision ) @@ -1,92 +1,0 @@ -md=squaremesh(model,1000000,1000000,5,5); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%redo the parameter file for this special shelf. -%constant thickness, constrained (vy=0) flow into an icefront, -%from 0 m/yr at the grounding line. - -%needed later -ymin=min(md.mesh.y); -ymax=max(md.mesh.y); -xmin=min(md.mesh.x); -xmax=max(md.mesh.x); - -di=md.materials.rho_ice/md.materials.rho_water; - -h=1000; -md.geometry.thickness=h*ones(md.mesh.numberofvertices,1); -md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; - -%Initial velocity and pressure -md.initialization.vx=zeros(md.mesh.numberofvertices,1); -md.initialization.vy=zeros(md.mesh.numberofvertices,1); -md.initialization.vz=zeros(md.mesh.numberofvertices,1); -md.initialization.pressure=zeros(md.mesh.numberofvertices,1); - -%Materials -md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); -md.materials.rheology_B=paterson(md.initialization.temperature); -md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); - -%Boundary conditions: -md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); -md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); -md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - -%constrain flanks to 0 normal velocity -pos=find(md.mesh.x==xmin | md.mesh.x==xmax); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvz(pos)=NaN; - -%constrain grounding line to 0 velocity -pos=find(md.mesh.y==ymin); -md.diagnostic.spcvx(pos)=0; -md.diagnostic.spcvy(pos)=0; - -%icefront -nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; -pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); -diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; -md.diagnostic.icefront=diagnostic.icefront; - -%partitioning -md.qmu.numberofpartitions=md.mesh.numberofvertices; -md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions); -md.qmu.partition=md.qmu.partition-1; - -%Dakota options -%variables -md.qmu.variables.rheology_B=normal_uncertain('scaled_MaterialsRheologyB',1,.5); - -%responses -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%method -md.qmu.method =dakota_method('nond_l'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver='diagnostic'; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; - -%imperative! -md.diagnostic.reltol=10^-10; %tighten for qmu analysese -md.qmu.isdakota=1; - -%solve -md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); - -%Fields and tolerances to track changes -md=tres(md,'dakota'); -md.results.dakota.importancefactors=importancefactors(md,'scaled_MaterialsRheologyB','MaxVel')'; -field_names ={'importancefactors'}; -field_tolerances={1e-10}; -field_values={... - md.results.dakota.importancefactors,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test237.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test237.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test239.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test239.m (revision 12167) +++ (revision ) @@ -1,17 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',120000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,2,1); -md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test241.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test241.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',120000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,2,1); -md.diagnostic.viscosity_overshoot=0.0; -md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test243.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test243.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.prognostic.hydrostatic_adjustment='Incremental'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test245.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test245.m (revision 12167) +++ (revision ) @@ -1,35 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; -md.cluster=none; -md.prognostic.hydrostatic_adjustment='Incremental'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test247.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test247.m (revision 12167) +++ (revision ) @@ -1,46 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.prognostic.hydrostatic_adjustment='Incremental'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test249.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test249.m (revision 12167) +++ (revision ) @@ -1,47 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; -md.cluster=none; -md.prognostic.hydrostatic_adjustment='Incremental'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test251.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test251.m (revision 12167) +++ (revision ) @@ -1,35 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.timestepping.time_adapt=1; -md.timestepping.final_time=10; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test253.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test253.m (revision 12167) +++ (revision ) @@ -1,49 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.timestepping.time_adapt=1; -md.timestepping.final_time=10; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... - 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... - 1e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test255.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test255.m (revision 12167) +++ (revision ) @@ -1,64 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -%Set up transient -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*-1 ]; - -md.surfaceforcings.mass_balance= smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; - -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ... - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'}; -field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; - -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(4).Vx),... - (md.results.TransientSolution(4).Vy),... - (md.results.TransientSolution(4).Vel),... - (md.results.TransientSolution(4).Pressure),... - (md.results.TransientSolution(4).Bed),... - (md.results.TransientSolution(4).Surface),... - (md.results.TransientSolution(4).Thickness),... - (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test257.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test257.m (revision 12167) +++ (revision ) @@ -1,64 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -%Set up transient -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*2 ]; - -md.surfaceforcings.mass_balance= smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; - -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ... - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'}; -field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; - -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(4).Vx),... - (md.results.TransientSolution(4).Vy),... - (md.results.TransientSolution(4).Vel),... - (md.results.TransientSolution(4).Pressure),... - (md.results.TransientSolution(4).Bed),... - (md.results.TransientSolution(4).Surface),... - (md.results.TransientSolution(4).Thickness),... - (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test259.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test259.m (revision 12167) +++ (revision ) @@ -1,69 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',350000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -%Set up transient -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*-1 ]; - -md.surfaceforcings.mass_balance= smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; - -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',... - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; - -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(4).Vx),... - (md.results.TransientSolution(4).Vy),... - (md.results.TransientSolution(4).Vz),... - (md.results.TransientSolution(4).Vel),... - (md.results.TransientSolution(4).Pressure),... - (md.results.TransientSolution(4).Bed),... - (md.results.TransientSolution(4).Surface),... - (md.results.TransientSolution(4).Thickness),... - (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test261.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test261.m (revision 12167) +++ (revision ) @@ -1,69 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',350000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -%Set up transient -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*2 ]; - -md.surfaceforcings.mass_balance= smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; - -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',... - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; - -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... - (md.results.TransientSolution(4).Vx),... - (md.results.TransientSolution(4).Vy),... - (md.results.TransientSolution(4).Vz),... - (md.results.TransientSolution(4).Vel),... - (md.results.TransientSolution(4).Pressure),... - (md.results.TransientSolution(4).Bed),... - (md.results.TransientSolution(4).Surface),... - (md.results.TransientSolution(4).Thickness),... - (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test263.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test263.m (revision 12167) +++ (revision ) @@ -1,28 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5, md.thermal.spctemperature+10, md.thermal.spctemperature+15; 1.5 2.5 3.5 4]; -md.timestepping.time_step=1; -md.timestepping.final_time=4; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3','Temperature4','BasalforcingsMeltingRate4'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - (md.results.TransientSolution(4).Temperature),... - (md.results.TransientSolution(4).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test265.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test265.m (revision 12167) +++ (revision ) @@ -1,62 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5; 1 2]; -md.timestepping.time_step=0.5; -md.timestepping.final_time=2; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3',... - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','BasalforcingsMeltingRate4'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... - 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... - 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... - 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - (md.results.TransientSolution(4).Vx),... - (md.results.TransientSolution(4).Vy),... - (md.results.TransientSolution(4).Vz),... - (md.results.TransientSolution(4).Vel),... - (md.results.TransientSolution(4).Pressure),... - (md.results.TransientSolution(4).Bed),... - (md.results.TransientSolution(4).Surface),... - (md.results.TransientSolution(4).Thickness),... - (md.results.TransientSolution(4).Temperature),... - (md.results.TransientSolution(4).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test267.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test267.m (revision 12167) +++ (revision ) @@ -1,72 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=generic('name',oshostname(),'np',3); - -md.timestepping.time_step=1; -md.settings.output_frequency=1; -md.timestepping.final_time=4; - -smb = ones(md.mesh.numberofvertices,1)*3.6; -smb=[ smb smb*-1 ]; - -md.surfaceforcings.mass_balance= smb; -md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; -md.transient.isthermal=0; -%Dakota options - -%partitioning -md.qmu.numberofpartitions=20; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); -md.qmu.partition=md.qmu.partition-1; - -%variables -md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,0.1); - -%responses -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.IceVolume=response_function('IceVolume',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.massFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%mass flux profiles -md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'}; -md.qmu.mass_flux_profile_directory=pwd; - -%% nond_sampling study -md.qmu.method=dakota_method('nond_samp'); -md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver=''; -md.qmu.params.analysis_components=''; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; -md.qmu.isdakota=1; - -md.diagnostic.reltol=10^-5; %tighten for qmu analyses -md.transient.requested_outputs=IceVolumeEnum(); - -%solve -md=solve(md,TransientSolutionEnum,'overwrite','y'); -md=tres(md,'dakota'); - -%Fields and tolerances to track changes -md.results.dakota.importancefactors=[]; -for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; -end -for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; -end -field_names ={'importancefactors'}; -field_tolerances={1e-11}; -field_values={... - md.results.dakota.importancefactors,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test301.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test301.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test303.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test303.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test305.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test305.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test307.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test307.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,2); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test309.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test309.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,5,2); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test311.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test311.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,4,2); -md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test313.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test313.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test315.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test315.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md.cluster=none; -md=setflowequation(md,'stokes','all'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test317.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test317.m (revision 12167) +++ (revision ) @@ -1,13 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test319.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test319.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=meshconvert(md); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.geometry.thickness; -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test321.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test321.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md=extrude(md,5,0.5); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test323.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test323.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.timestepping.time_step=0; -md.cluster=none; -md=solve(md,ThermalSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.ThermalSolution.Temperature),... - (md.results.ThermalSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test325.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test325.m (revision 12167) +++ (revision ) @@ -1,19 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test327.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test327.m (revision 12167) +++ (revision ) @@ -1,37 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1',... - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2',... - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test329.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test329.m (revision 12167) +++ (revision ) @@ -1,47 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,5,1.2); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test331.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test331.m (revision 12167) +++ (revision ) @@ -1,33 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test333.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test333.m (revision 12167) +++ (revision ) @@ -1,47 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test335.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test335.m (revision 12167) +++ (revision ) @@ -1,23 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,4,1); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; - -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 -}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test337.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test337.m (revision 12167) +++ (revision ) @@ -1,33 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=0*2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.FrictionCoefficient),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test339.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test339.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.FrictionCoefficient),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test341.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test341.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.FrictionCoefficient),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test343.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test343.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[104*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.FrictionCoefficient),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test345.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test345.m (revision 12167) +++ (revision ) @@ -1,35 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.timestepping.time_adapt=1; -md.timestepping.final_time=600; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test347.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test347.m (revision 12167) +++ (revision ) @@ -1,49 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,4,1.2); -md=setflowequation(md,'hutter','all'); -md.cluster=none; -md.timestepping.time_adapt=1; -md.timestepping.final_time=500; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; - %'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... -% (md.results.TransientSolution(3).Vx),... -% (md.results.TransientSolution(3).Vy),... -% (md.results.TransientSolution(3).Vz),... -% (md.results.TransientSolution(3).Vel),... -% (md.results.TransientSolution(3).Pressure),... -% (md.results.TransientSolution(3).Bed),... -% (md.results.TransientSolution(3).Surface),... -% (md.results.TransientSolution(3).Thickness),... -% (md.results.TransientSolution(3).Temperature),... -% (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test349.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test349.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md.timestepping.time_step=0; -md.cluster=none; -md=solve(md,EnthalpySolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Enthalpy','Waterfraction','Temperature'}; -field_tolerances={1e-13,1e-13,1e-13}; -field_values={... - (md.results.EnthalpySolution.Enthalpy),... - (md.results.EnthalpySolution.Waterfraction),... - (md.results.EnthalpySolution.Temperature),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test351.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test351.m (revision 12167) +++ (revision ) @@ -1,30 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md.thermal.isenthalpy=1; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Enthalpy1','Waterfraction1','Temperature1',... - 'Enthalpy2','Waterfraction2','Temperature2',... - 'Enthalpy3','Waterfraction3','Temperature3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Enthalpy),... - (md.results.TransientSolution(1).Waterfraction),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(2).Enthalpy),... - (md.results.TransientSolution(2).Waterfraction),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(3).Enthalpy),... - (md.results.TransientSolution(3).Waterfraction),... - (md.results.TransientSolution(3).Temperature),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test353.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test353.m (revision 12167) +++ (revision ) @@ -1,55 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md.initialization.temperature(:)=272; -md.thermal.spctemperature(find(md.mesh.vertexonsurface))=272; -md.thermal.isenthalpy=1; -md.basalforcings.geothermalflux(:)=5; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'}; -field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... - 1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).Enthalpy),... - (md.results.TransientSolution(1).Waterfraction),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).Enthalpy),... - (md.results.TransientSolution(2).Waterfraction),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).Enthalpy),... - (md.results.TransientSolution(3).Waterfraction),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test401.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test401.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test403.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test403.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,4,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test405.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test405.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test407.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test407.m (revision 12167) +++ (revision ) @@ -1,17 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test409.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test409.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test411.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test411.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,4,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,ThermalSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.ThermalSolution.Temperature),... - (md.results.ThermalSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test413.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test413.m (revision 12167) +++ (revision ) @@ -1,19 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,4,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test415.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test415.m (revision 12167) +++ (revision ) @@ -1,33 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test417.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test417.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; -field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - (md.results.TransientSolution(3).Vx),... - (md.results.TransientSolution(3).Vy),... - (md.results.TransientSolution(3).Vz),... - (md.results.TransientSolution(3).Vel),... - (md.results.TransientSolution(3).Pressure),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).Temperature),... - (md.results.TransientSolution(3).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test419.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test419.m (revision 12167) +++ (revision ) @@ -1,22 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 -}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test421.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test421.m (revision 12167) +++ (revision ) @@ -1,21 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test423.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test423.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',300000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%partitioning -md.qmu.numberofpartitions=md.mesh.numberofvertices; -md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions); -md.qmu.partition=md.qmu.partition-1; -md.qmu.isdakota=1; - -%Dakota options -%variables -md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); -md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01); -%md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01*ones(md.qmu.numberofpartitions,1)); - -%responses -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%method -md.qmu.method =dakota_method('nond_l'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver='diagnostic'; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; - - -%imperative! -md.diagnostic.reltol=10^-5; %tighten for qmu analysese - -%solve -md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); - -%Fields and tolerances to track changes -md=tres(md,'dakota'); -md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')'; -field_names ={'importancefactors'}; -field_tolerances={1e-10}; -field_values={... - md.results.dakota.importancefactors,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test425.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test425.m (revision 12167) +++ (revision ) @@ -1,45 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%Dakota options - -%partitioning -md.qmu.numberofpartitions=20; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); -md.qmu.partition=md.qmu.partition-1; - -%variables -md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); -md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01); - -%responses -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%method -md.qmu.method =dakota_method('nond_l'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver='diagnostic'; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; - - -%imperative! -md.diagnostic.reltol=10^-5; %tighten for qmu analyses -md.qmu.isdakota=1; - -%solve -md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); - -%Fields and tolerances to track changes -md=tres(md,'dakota'); -md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')'; -field_names ={'importancefactors'}; -field_tolerances={1e-10}; -field_values={... - md.results.dakota.importancefactors,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test427.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test427.m (revision 12167) +++ (revision ) @@ -1,71 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.materials.rho_ice=10^7; %involved in the mass flux, make it easy -md.geometry.thickness(:)=1; %make it easy - -%constrain all velocities to 1 m/yr, in the y-direction -md.diagnostic.spcvx(:)=0; -md.diagnostic.spcvy(:)=1; -md.diagnostic.spcvz(:)=0; - -%Dakota options - -%partitioning -md.qmu.numberofpartitions=20; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); -md.qmu.partition=md.qmu.partition-1; - -%variables -md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01); - -%responses -md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); -md.qmu.responses.MassFlux7=response_function('indexed_MassFlux_7',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%mass flux profiles -md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'}; -md.qmu.mass_flux_profile_directory=pwd; - -%method -md.qmu.method =dakota_method('nond_l'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver='diagnostic'; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; -md.qmu.isdakota=1; -md.diagnostic.reltol=10^-5; %tighten for qmu analyses - -%solve -md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); -md=tres(md,'dakota'); - -%Fields and tolerances to track changes - -%ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr -%we recover those mass fluxes through the mean of the response. -%also, we recover the max velo, which should be 1m/yr. -%we put all that data in the importancefactors, which we will use to test for success. -%also, check that the stddev are 0. -md.results.dakota.importancefactors=[]; -for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; -end -for i=1:8, - md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; -end -field_names ={'importancefactors'}; -field_tolerances={1e-11}; -field_values={... - md.results.dakota.importancefactors,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test429.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test429.m (revision 12167) +++ (revision ) @@ -1,38 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',170000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.timestepping.time_step=0; -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.SteadystateSolution.Gradient1),... - md.results.SteadystateSolution.J,... - (md.results.SteadystateSolution.FrictionCoefficient),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test431.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test431.m (revision 12167) +++ (revision ) @@ -1,38 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',170000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); -md.timestepping.time_step=0; -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; -field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; -field_values={... - (md.results.SteadystateSolution.Gradient1),... - md.results.SteadystateSolution.J,... - (md.results.SteadystateSolution.FrictionCoefficient),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test435.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test435.m (revision 12167) +++ (revision ) @@ -1,21 +1,0 @@ -%test partitioning, and partition averaging -md=triangle(model,'../Exp/Square.exp',30000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%partitioning -md.qmu.numberofpartitions=100; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions); -md.qmu.partition=md.qmu.partition-1; - -vector=(1:1:md.mesh.numberofvertices)'; -vector_on_partition=AreaAverageOntoPartition(md,vector); -vector_on_nodes=vector_on_partition(md.qmu.partition+1); - -field_names ={'vector_on_nodes'}; -field_tolerances={1e-11}; -field_values={... - vector_on_nodes,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test437.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test437.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test439.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test439.m (revision 12167) +++ (revision ) @@ -1,49 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',200000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -%partitioning -md.qmu.numberofpartitions=10; -md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions); -md.qmu.partition=md.qmu.partition-1; -md.qmu.isdakota=1; - -%Dakota options -%variables -md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); - -%responses -md.qmu.responses.MaxVel=response_function('scaled_Thickness',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); - -%method -md.qmu.method =dakota_method('nond_l'); - -%parameters -md.qmu.params.direct=true; -md.qmu.params.analysis_driver='diagnostic'; -md.qmu.params.evaluation_concurrency=1; -md.qmu.params.interval_type='forward'; - - -%imperative! -md.diagnostic.reltol=10^-5; %tighten for qmu analysese - -%solve -md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); -md=tres(md,'dakota'); - -%test on thickness -h=zeros(md.qmu.numberofpartitions,1); -for i=1:md.qmu.numberofpartitions, - h(i)=md.qmu.results.dresp_out(i).mean; -end - -%project onto grid -thickness=h(md.qmu.partition+1); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-11}; -field_values={thickness}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test441.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test441.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test443.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test443.m (revision 12167) +++ (revision ) @@ -1,19 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','tiling'); -md.cluster=none; -md.diagnostic.reltol=0.4; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-06,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test445.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test445.m (revision 12167) +++ (revision ) @@ -1,37 +1,0 @@ -radius=1e6; -shelfextent=2e5; - -md=roundmesh(model,radius,200000); -%fix center node to 0,0 -rad=sqrt(md.mesh.x.^2+md.mesh.y.^2); -pos=find(rad==min(rad)); -md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center -xelem=md.mesh.x(md.mesh.elements)*[1;1;1]/3; -yelem=md.mesh.y(md.mesh.elements)*[1;1;1]/3; -rad=sqrt(xelem.^2+yelem.^2); -flags=zeros(md.mesh.numberofelements,1); -pos=find(rad>=(radius-shelfextent)); -flags(pos)=1; -md=setmask(md,flags,''); -md=parameterize(md,'../Par/RoundSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; - -md.transient.isthermal=0; -md.transient.isprognostic=0; -md.transient.isdiagnostic=0; -md.transient.isgroundingline=1; - -%test different grounding line dynamics -md.groundingline.migration='AgressiveMigration'; -md=solve(md,TransientSolutionEnum); -element_on_iceshelf_agressive=(md.results.TransientSolution.MaskElementonfloatingice); - -md.groundingline.migration='SoftMigration'; -md=solve(md,TransientSolutionEnum); -element_on_iceshelf_soft=(md.results.TransientSolution.MaskElementonfloatingice); - -%Fields and tolerances to track changes -field_names ={'ElementOnIceShelfAgressive','ElementOnIceShelfSoft'}; -field_tolerances={1e-13,1e-13}; -field_values={element_on_iceshelf_agressive,element_on_iceshelf_soft}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test447.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test447.m (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.initialization.vx(:)=0; -md.initialization.vy(:)=0; -md.initialization.vel(:)=0; -md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; -md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; -md.geometry.thickness(:)=1000; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md.surfaceforcings.mass_balance(:)=100; -md.transient.isdiagnostic=0; -md.transient.isgroundingline=1; -md.groundingline.migration='AgressiveMigration'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... - 'Bed2','Surface2','Thickness2','Floatingice2',... - 'Bed3','Surface3','Thickness3','Floatingice3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).MaskElementonfloatingice),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).MaskElementonfloatingice),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).MaskElementonfloatingice),... - }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test448.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test448.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test448.m (revision 12168) @@ -3,5 +3,4 @@ md=parameterize(md,'../Par/SquareSheetShelf.par'); md=setflowequation(md,'macayeal','all'); -md.cluster=none; md.initialization.vx(:)=0; md.initialization.vy(:)=0; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test449.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test449.m (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.initialization.vx(:)=0; -md.initialization.vy(:)=0; -md.initialization.vel(:)=0; -md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; -md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; -md.geometry.thickness(:)=1300; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md.surfaceforcings.mass_balance(:)=-150; -md.transient.isdiagnostic=0; -md.transient.isgroundingline=1; -md.groundingline.migration='SoftMigration'; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... - 'Bed2','Surface2','Thickness2','Floatingice2',... - 'Bed3','Surface3','Thickness3','Floatingice3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).MaskElementonfloatingice),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).MaskElementonfloatingice),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).MaskElementonfloatingice),... - }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test450.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test450.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test450.m (revision 12168) @@ -3,5 +3,4 @@ md=parameterize(md,'../Par/SquareSheetShelf.par'); md=setflowequation(md,'macayeal','all'); -md.cluster=none; md.initialization.vx(:)=0; md.initialization.vy(:)=0; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test451.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test451.m (revision 12167) +++ (revision ) @@ -1,42 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',350000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md.cluster=none; -md.initialization.vx(:)=0; -md.initialization.vy(:)=0; -md.initialization.vel(:)=0; -md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; -md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; -md.geometry.thickness(:)=1000; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md.surfaceforcings.mass_balance(:)=100; -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -md.transient.isdiagnostic=0; -md.transient.isgroundingline=1; -md.groundingline.migration='AgressiveMigration'; - -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... - 'Bed2','Surface2','Thickness2','Floatingice2',... - 'Bed3','Surface3','Thickness3','Floatingice3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).MaskElementonfloatingice),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).MaskElementonfloatingice),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).MaskElementonfloatingice),... - }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test452.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test452.m (revision 12167) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test452.m (revision 12168) @@ -2,5 +2,4 @@ md=setmask(md,'../Exp/SquareShelf.exp',''); md=parameterize(md,'../Par/SquareSheetShelf.par'); -md.cluster=none; md.initialization.vx(:)=0; md.initialization.vy(:)=0; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test453.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test453.m (revision 12167) +++ (revision ) @@ -1,41 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md.initialization.vx(:)=0; -md.initialization.vy(:)=0; -md.initialization.vel(:)=0; -md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; -md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; -md.geometry.thickness(:)=1300; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -md.surfaceforcings.mass_balance(:)=-150; -md.transient.isdiagnostic=0; -md.transient.isgroundingline=1; -md.groundingline.migration='SoftMigration'; -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... - 'Bed2','Surface2','Thickness2','Floatingice2',... - 'Bed3','Surface3','Thickness3','Floatingice3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13,... - 1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).MaskElementonfloatingice),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).MaskElementonfloatingice),... - (md.results.TransientSolution(3).Bed),... - (md.results.TransientSolution(3).Surface),... - (md.results.TransientSolution(3).Thickness),... - (md.results.TransientSolution(3).MaskElementonfloatingice),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test455.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test455.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'macayeal','all'); -md.diagnostic.isnewton=1; -md.diagnostic.restol=0.0001; -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test457.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test457.m (revision 12167) +++ (revision ) @@ -1,20 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,5,1); -md=setflowequation(md,'pattyn','all'); -md.diagnostic.isnewton=1; -md.diagnostic.restol=0.0001; -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test459.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test459.m (revision 12167) +++ (revision ) @@ -1,19 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',180000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); -md.diagnostic.isnewton=1; -md.diagnostic.restol=0.0001; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test461.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test461.m (revision 12167) +++ (revision ) @@ -1,24 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.timestepping.time_step=0; -md.thermal.isenthalpy=1; -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; -field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.Waterfraction),... - (md.results.SteadystateSolution.Enthalpy),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test463.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test463.m (revision 12167) +++ (revision ) @@ -1,24 +1,0 @@ -md=triangle(model,'../Exp/Square.exp',150000); -md=setmask(md,'../Exp/SquareShelf.exp',''); -md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=extrude(md,3,2); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.timestepping.time_step=0; -md.thermal.isenthalpy=1; -md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; -field_tolerances={1e-09,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.Waterfraction),... - (md.results.SteadystateSolution.Enthalpy),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test501.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test501.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test503.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test503.m (revision 12167) +++ (revision ) @@ -1,18 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,0.9); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test505.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test505.m (revision 12167) +++ (revision ) @@ -1,17 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,0.9); -md=setflowequation(md,'stokes','all'); -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy),... - (md.results.DiagnosticSolution.Vz),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Pressure),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test507.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test507.m (revision 12167) +++ (revision ) @@ -1,26 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test509.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test509.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; -field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test511.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test511.m (revision 12167) +++ (revision ) @@ -1,35 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,2,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... - 1e-12,1e-12,1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test513.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test513.m (revision 12167) +++ (revision ) @@ -1,35 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,2,1); -md=setflowequation(md,'stokes','all'); -md.cluster=none; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -%The thickness wants to be lower than 1 so we contrain it to 1 -field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; -field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08}; -field_values={... - (md.results.TransientSolution(1).Vx),... - (md.results.TransientSolution(1).Vy),... - (md.results.TransientSolution(1).Vz),... - (md.results.TransientSolution(1).Vel),... - (md.results.TransientSolution(1).Pressure),... - (md.results.TransientSolution(1).Bed),... - (md.results.TransientSolution(1).Surface),... - (md.results.TransientSolution(1).Thickness),... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Vx),... - (md.results.TransientSolution(2).Vy),... - (md.results.TransientSolution(2).Vz),... - (md.results.TransientSolution(2).Vel),... - (md.results.TransientSolution(2).Pressure),... - (md.results.TransientSolution(2).Bed),... - (md.results.TransientSolution(2).Surface),... - (md.results.TransientSolution(2).Thickness),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test515.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test515.m (revision 12167) +++ (revision ) @@ -1,22 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,4,1.1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 -}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test517.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test517.m (revision 12167) +++ (revision ) @@ -1,22 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 -}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test519.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test519.m (revision 12167) +++ (revision ) @@ -1,22 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,2,1); -md=setflowequation(md,'stokes','all'); -md.cluster=none; -md.timestepping.time_step=0; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06 -}; -field_values={... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test521.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test521.m (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',10000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); - -%impose hydrostatic equilibrium (required by Stokes) -md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; -md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md=extrude(md,3,1); -md=setflowequation(md,'stokes','all'); -md=modelextract(md,md.mask.elementonfloatingice); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'MaterialsRheologyBbar'}; -md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10^8*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'MaterialsRheologyB' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.MaterialsRheologyB),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test523.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test523.m (revision 12167) +++ (revision ) @@ -1,34 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',20000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; - -md.cluster=none; -md=solve(md,DiagnosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; -field_tolerances={1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11}; -field_values={... - (md.results.DiagnosticSolution.Gradient1),... - md.results.DiagnosticSolution.J,... - (md.results.DiagnosticSolution.FrictionCoefficient),... - (md.results.DiagnosticSolution.Pressure),... - (md.results.DiagnosticSolution.Vel),... - (md.results.DiagnosticSolution.Vx),... - (md.results.DiagnosticSolution.Vy) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test525.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test525.m (revision 12167) +++ (revision ) @@ -1,39 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.iscontrol=1; -md.inversion.control_parameters={'FrictionCoefficient'}; -md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); -md.inversion.nsteps=2; -md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; -md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); -md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; -md.timestepping.time_step=0; - -md.thermal.penalty_lock=5; -md.cluster=none; -md=solve(md,SteadystateSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={... - (md.results.SteadystateSolution.Gradient1),... - md.results.SteadystateSolution.J,... - (md.results.SteadystateSolution.FrictionCoefficient),... - (md.results.SteadystateSolution.Pressure),... - (md.results.SteadystateSolution.Vel),... - (md.results.SteadystateSolution.Vx),... - (md.results.SteadystateSolution.Vy),... - (md.results.SteadystateSolution.Vz),... - (md.results.SteadystateSolution.Temperature),... - (md.results.SteadystateSolution.BasalforcingsMeltingRate) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test527.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test527.m (revision 12167) +++ (revision ) @@ -1,56 +1,0 @@ -%Simple mesh 1 -hVertices=10000*ones(27,1); -hVertices(1:5)=1000; -md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000,'hVertices',hVertices,'gradation',3,'geometricalmetric',1); -x1=md.mesh.x; -y1=md.mesh.y; - -%Simple mesh 2 -md=bamg(model,'domain','../Exp/Pig.exp','hmax',10000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -x2=md.mesh.x; -y2=md.mesh.y; - -%refine existing mesh 1 -hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node'); -metric=ComputeMetric(hessian,2/9,1,1000,25*10^3,[]); -md.miscellaneous.dummy=metric; -md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1); -x3=md2.mesh.x; -y3=md2.mesh.y; - -%refine existing mesh 2 -md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1); -x4=md2.mesh.x; -y4=md2.mesh.y; - -%refine existing mesh 3 -hVertices=NaN*ones(md.mesh.numberofvertices,1); -hVertices(find(md.mesh.vertexonboundary))=500; -md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1,'hVertices',hVertices); -x5=md2.mesh.x; -y5=md2.mesh.y; - -%refine existing mesh 4 -md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',0,'err',1); -x6=md2.mesh.x; -y6=md2.mesh.y; - -%refine existing mesh 5 -md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); -x7=md2.mesh.x; -y7=md2.mesh.y; - -%Fields and tolerances to track changes -field_names ={'x1' 'y1' 'x2' 'y2' 'x3' 'y3' 'x4' 'y4' 'x5' 'y5' 'x6' 'y6' 'x7' 'y7' }; -field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13}; -field_values={... - x1, y1,... - y2, y2,... - y3, y3,... - y4, y4,... - y5, y5,... - y6, y6,... - y7, y7,... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test529.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test529.m (revision 12167) +++ (revision ) @@ -1,22 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.thermal.stabilization=2; -md.transient.isdiagnostic=0; -md.transient.isprognostic=0; -md.transient.isthermal=1; -md.transient.isgroundingline=0; -md=solve(md,TransientSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature1','BasalforcingsMeltingRate1', ... - 'Temperature2','BasalforcingsMeltingRate2'}; -field_tolerances={1e-13,1e-9,1e-13,1e-9}; -field_values={... - (md.results.TransientSolution(1).Temperature),... - (md.results.TransientSolution(1).BasalforcingsMeltingRate),... - (md.results.TransientSolution(2).Temperature),... - (md.results.TransientSolution(2).BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test531.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test531.m (revision 12167) +++ (revision ) @@ -1,17 +1,0 @@ -md=triangle(model,'../Exp/Pig.exp',30000); -md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); -md=parameterize(md,'../Par/Pig.par'); -md=extrude(md,3,1); -md=setflowequation(md,'pattyn','all'); -md.thermal.stabilization=2; -md.timestepping.time_step=0; -md.thermal.penalty_threshold=40; -md=solve(md,ThermalSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Temperature','BasalforcingsMeltingRate'}; -field_tolerances={1e-13,1e-12}; -field_values={... - (md.results.ThermalSolution.Temperature),... - (md.results.ThermalSolution.BasalforcingsMeltingRate),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test601.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test601.m (revision 12167) +++ (revision ) @@ -1,13 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test603.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test603.m (revision 12167) +++ (revision ) @@ -1,16 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=meshconvert(md); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.geometry.thickness; -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test605.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test605.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=extrude(md,6,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,PrognosticSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.PrognosticSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test607.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test607.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,SurfaceSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... - (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test609.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test609.m (revision 12167) +++ (revision ) @@ -1,15 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=extrude(md,5,1.5); -md=setflowequation(md,'pattyn','all'); -md.cluster=none; -md=solve(md,SurfaceSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... - (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test611.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test611.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BedSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'BedSlopeX','BedSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.BedSlopeSolution.BedSlopeX),... - (md.results.BedSlopeSolution.BedSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test613.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test613.m (revision 12167) +++ (revision ) @@ -1,15 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=extrude(md,2,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BedSlopeSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'BedSlopeX','BedSlopeY'}; -field_tolerances={1e-13,1e-13}; -field_values={... - (md.results.BedSlopeSolution.BedSlopeX),... - (md.results.BedSlopeSolution.BedSlopeY),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test615.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test615.m (revision 12167) +++ (revision ) @@ -1,13 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test617.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test617.m (revision 12167) +++ (revision ) @@ -1,15 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=meshconvert(md); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); -md.balancethickness.stabilization=3; -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test619.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test619.m (revision 12167) +++ (revision ) @@ -1,14 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=extrude(md,3,1); -md=setflowequation(md,'macayeal','all'); -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Thickness'}; -field_tolerances={1e-13}; -field_values={... - (md.results.BalancethicknessSolution.Thickness),... - }; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test621.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test621.m (revision 12167) +++ (revision ) @@ -1,31 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.nsteps=2; -md.prognostic.stabilization=1; -md.inversion.iscontrol=1; -md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.geometry.thickness; -md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1); -md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); - -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'}; -field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; -field_values={... - (md.results.BalancethicknessSolution.Gradient1),... - md.results.BalancethicknessSolution.J,... - (md.results.BalancethicknessSolution.BalancethicknessThickeningRate),... - (md.results.BalancethicknessSolution.Thickness) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test623.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test623.m (revision 12167) +++ (revision ) @@ -1,32 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=meshconvert(md); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); - -%control parameters -md.inversion.nsteps=2; -md.balancethickness.stabilization=3; -md.inversion.iscontrol=1; -md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.geometry.thickness; -md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1); -md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1); -md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1); -md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); - -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'}; -field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; -field_values={... - (md.results.BalancethicknessSolution.Gradient1),... - md.results.BalancethicknessSolution.J,... - (md.results.BalancethicknessSolution.BalancethicknessThickeningRate),... - (md.results.BalancethicknessSolution.Thickness) -}; Index: sm/branches/trunk-jpl-damage/test/NightlyRun/test625.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test625.m (revision 12167) +++ (revision ) @@ -1,40 +1,0 @@ -md=triangle(model,'../Exp/79North.exp',10000); -md=meshconvert(md); -md=setmask(md,'../Exp/79NorthShelf.exp',''); -md=parameterize(md,'../Par/79North.par'); -md=setflowequation(md,'macayeal','all'); - -%Ice sheet only -md=modelextract(md,md.mask.elementongroundedice); -pos=find(md.mesh.vertexonboundary); -md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); - -%control parameters -md.inversion.thickness_obs=md.geometry.thickness; -md.inversion.iscontrol=1; -md.inversion.thickness_obs=md.geometry.thickness; -md.inversion.nsteps=2; -md.inversion.control_parameters={'Vx' 'Vy'}; -md.balancethickness.stabilization=1; -md.inversion.gradient_scaling=[10/md.constants.yts*ones(md.inversion.nsteps,1) 10/md.constants.yts*ones(md.inversion.nsteps,1)]; -md.inversion.min_parameters=[-2000*ones(md.mesh.numberofvertices,1) -2000*ones(md.mesh.numberofvertices,1)]; -md.inversion.max_parameters=[+2000*ones(md.mesh.numberofvertices,1) +2000*ones(md.mesh.numberofvertices,1)]; -md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); -md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); -md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); -md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); - -md.cluster=none; -md=solve(md,BalancethicknessSolutionEnum); - -%Fields and tolerances to track changes -field_names ={'Gradient1' 'Gradient2' 'Misfits' 'Vx' 'Vy' 'Thickness'}; -field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; -field_values={... - (md.results.BalancethicknessSolution.Gradient1),... - (md.results.BalancethicknessSolution.Gradient2),... - md.results.BalancethicknessSolution.J,... - (md.results.BalancethicknessSolution.Vx),... - (md.results.BalancethicknessSolution.Vy),... - (md.results.BalancethicknessSolution.Thickness) -}; Index: /issm/branches/trunk-jpl-damage/test/Par/SquareShelfConstrained.py =================================================================== --- /issm/branches/trunk-jpl-damage/test/Par/SquareShelfConstrained.py (revision 12168) +++ /issm/branches/trunk-jpl-damage/test/Par/SquareShelfConstrained.py (revision 12168) @@ -0,0 +1,59 @@ +from numpy import * +from verbose import * +import scipy.io as matio +import InterpFromMeshToMesh2d as im +from paterson import * + +#Start defining model parameters here +#Geometry +hmin = 300. +hmax = 1000. +ymin = min(md.mesh.y) +ymax = max(md.mesh.y) + +md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin) +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface = md.geometry.bed+md.geometry.thickness + +#Initial velocity +mat=matio.loadmat('../Data/SquareShelfConstrained.data') +#deal with 'F' oriented matlab matrices! +index=mat['index'].astype(float) +index=reshape(index.T,(len(index),3),order='F') + +md.initialization.vx = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vx'], md.mesh.x, md.mesh.y) +md.initialization.vy = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vy'], md.mesh.x, md.mesh.y) +md.initialization.vz = zeros(md.mesh.numberofvertices) +md.initialization.pressure = zeros(md.mesh.numberofvertices) +#Materials +md.initialization.temperature = (273.-20)*ones(md.mesh.numberofvertices) +md.materials.rheology_B = paterson(md.initialization.temperature) +md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) +#Surface mass balance and basal melting +md.surfaceforcings.mass_balance = 10.*ones(md.mesh.numberofvertices) +md.basalforcings.melting_rate = 5.*ones(md.mesh.numberofvertices) +#Friction +pos = nonzero(md.mask.elementonfloatingice) +md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) +md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] =0. +md.friction.p = ones(md.mesh.numberofelements) +md.friction.q = ones(md.mesh.numberofelements) +#Numerical parameters +md.diagnostic.viscosity_overshoot = 0.0 +md.prognostic.stabilization = 1. +md.thermal.stabilization = 1. +md.verbose = verbose() +md.settings.waitonlock = 30. +md.diagnostic.restol = 0.05 +md.diagnostic.reltol = 0.05 +md.steadystate.reltol = 0.05 +md.diagnostic.abstol = nan +md.timestepping.time_step = 1. +md.timestepping.final_time = 3. +#Deal with boundary conditions: +md = SetIceShelfBC(md) +#Change name so that no test have the same name +A = dbstack +if length(A) > 2.: + md.miscellaneous.name = A[2].file[0:0-2.] +